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#* Bio::FlatFileIndex::Results
#+ Bio::RestrictionEnzyme::DenseIntArray
#+ Bio::Sequence::Common
#+ Bio::RestrictionEnzyme::SortedNumArray
#+ Bio::FlatFileIndex::Results
#<< Bio::Sequence::Common
#<< Bio::RestrictionEnzyme::DenseIntArray
#<< Bio::FlatFileIndex::Indexer::NameSpaces
#<< Bio::RestrictionEnzyme::SortedNumArray
#<< Bio::Alignment::OriginalAlignment
#<=> Bio::PDB::Model
#<=> Bio::PDB::Chain
#<=> Bio::Relation
#<=> Bio::PDB::Record::ATOM
#<=> Bio::PDB::Residue
#<=> Bio::Location
#<=> Bio::Map::Mapping
#== Bio::GFF::GFF2::Record::Value
#== Bio::Blast::NCBIOptions
#== Bio::Location
#== Bio::RestrictionEnzyme::DenseIntArray
#== Bio::FlatFileIndex::Flat_1::Record
#== Bio::GFF::GFF2::Record
#== Bio::GFF::GFF2::MetaData
#== Bio::Alignment::OriginalAlignment
#== Bio::GFF::GFF3::SequenceRegion
#== Bio::Reference
#== Bio::GFF::GFF3::Record::Target
#== Bio::GFF::GFF3::Record::Gap
#== Bio::Locations
#== Bio::RestrictionEnzyme::SortedNumArray
#=== Bio::Relation
#Pdb_LString Bio::PDB::DataType::ConstLikeMethod
#Pdb_Real Bio::PDB::DataType::ConstLikeMethod
#Pdb_String Bio::PDB::DataType::ConstLikeMethod
#[] Bio::PDB::Model
#[] Bio::NucleicAcid::Data
#[] Bio::RestrictionEnzyme::SortedNumArray
#[] Bio::Features
#[] Bio::Feature
#[] Bio::CodonTable
[] Bio::RestrictionEnzyme::DenseIntArray
[] Bio::FlatFile::AutoDetect::RuleTemplate
[] Bio::PDB::Coordinate
[] Bio::PDB::DataType::Pdb_Real
#[] Bio::AAindex2
#[] Bio::Alignment::OriginalAlignment
[] Bio::ColorScheme::Simple
#[] Bio::Locations
#[] Bio::PDB
[] Bio::CodonTable
#[] Bio::FastaNumericFormat
#[] Bio::PDB::Chain
[] Bio::PDB::DataType::Pdb_String
#[] Bio::PDB::Residue
#[] Bio::FANTOM::MaXML::Sequences
#[] Bio::SOFT::Samples
[] Bio::ColorScheme::Score
[] Bio::RestrictionEnzyme::SortedNumArray
#[] Bio::FlatFileIndex::BDBwrapper
#[] Bio::FANTOM::MaXML::Annotations
#[] Bio::AminoAcid::Data
#[] Bio::RestrictionEnzyme::DenseIntArray
[] Bio::PDB::DataType::Pdb_LString
#[] Bio::FlatFileIndex::FileIDs
#[] Bio::PhyloXML::Parser
#[] Bio::SOFT::Table::Row
[] Bio::FlatFile::AutoDetect
#[]= Bio::FlatFileIndex::BDBwrapper
#[]= Bio::Registry::DB
#[]= Bio::RestrictionEnzyme::SortedNumArray
#[]= Bio::FlatFileIndex::FileIDs
#[]= Bio::RestrictionEnzyme::DenseIntArray
#[]= Bio::CodonTable
#__output_phylip_common Bio::Alignment::Output
#__store__ Bio::Alignment::OriginalAlignment
_call_command_popen_jruby19 Bio::Command
_call_command_popen_ruby18 Bio::Command
_call_command_popen_ruby19 Bio::Command
#aa Bio::Sequence
#aalen Bio::NBRF
#aalen Bio::FastaFormat
#aalen Bio::KEGG::GENES
#aaref Bio::PAML::Codeml::PositiveSite
#aaseq Bio::KEGG::GENES
aaseq Bio::DBGET
#aaseq Bio::NBRF
#aaseq Bio::FastaFormat
#aaseq Bio::GCG::Seq
#aaseq Bio::Genscan::Report::Gene
#aaseq Bio::PDB::Chain
#aaseqline Bio::Spidey::Report::SegmentPair
#ab Bio::MEDLINE
#abbrev Bio::KEGG::Keggtab::DB
#absent Bio::PhyloXML::BinaryCharacters
#absent_count Bio::PhyloXML::BinaryCharacters
#absolute Bio::Locations
#abstract Bio::Reference
#ac Bio::EMBLDB::Common
#ac Bio::TRANSFAC
#ac Bio::PROSITE
acc2hit Bio::Hinv
#acc_version Bio::NCBIDB::Common
#acc_version Bio::FastaFormat
#acc_version Bio::FastaDefline
#acceptor_score Bio::Genscan::Report::Exon
#accession Bio::PDB
#accession Bio::FastaDefline
#accession Bio::PhyloXML::Sequence
#accession Bio::HMMER::Report::Hit
#accession Bio::Blast::Report::Hit
#accession Bio::FastaFormat
#accession Bio::EMBLDB::Common
#accession Bio::HMMER::Report::Hsp
#accession Bio::NCBIDB::Common
#accession Bio::Iprscan::Report::Match
#accessions Bio::FastaDefline
#accessions Bio::FastaFormat
#accessions Bio::NCBIDB::Common
#accessions Bio::Sequence
acos Bio::PDB::Utils
#activity Bio::KEGG::DRUG
#ad Bio::MEDLINE
adapter Bio::Sequence
#add Bio::FlatFileIndex::BDB_1::BDBMappingFile
#add Bio::FlatFile::AutoDetect
#add Bio::FlatFileIndex::FileIDs
#add Bio::FlatFileIndex::Indexer::NameSpaces
#addAtom Bio::PDB::Residue
#addChain Bio::PDB::Model
#addLigand Bio::PDB::Chain
#addModel Bio::PDB
#addResidue Bio::PDB::Chain
#addSolvent Bio::PDB::Model
#add_attribute Bio::GFF::GFF2::Record
#add_continuation Bio::PDB::Record
#add_cut_range Bio::RestrictionEnzyme::Range::SequenceRange
#add_cut_ranges Bio::RestrictionEnzyme::Range::SequenceRange
#add_cuts_from_cut_ranges Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#add_defline Bio::FastaDefline
#add_edge Bio::Tree
#add_exclusive Bio::FlatFileIndex::BDB_1::BDBMappingFile
#add_header Bio::SOFT::Table
#add_header_line Bio::Fastq
#add_header_line Bio::Blat::Report
#add_header_or_row Bio::SOFT::Table
#add_horizontal_cut_range Bio::RestrictionEnzyme::Range::SequenceRange
#add_line Bio::Fastq
#add_line Bio::Blat::Report
#add_mapping_as_map Bio::Map::ActsLikeMap
#add_mapping_as_marker Bio::Map::ActsLikeMarker
#add_node Bio::Tree
#add_nr Bio::FlatFileIndex::BDB_1::BDBMappingFile
#add_options Bio::Blast::NCBIOptions
#add_overwrite Bio::FlatFileIndex::BDB_1::BDBMappingFile
#add_record Bio::FlatFileIndex::Flat_1::FlatMappingFile
#add_row Bio::SOFT::Table
#add_secondary_namespaces Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#add_seq Bio::Alignment::OriginalAlignment
#add_sequences Bio::Alignment::OriginalAlignment
#add_spacing Bio::RestrictionEnzyme::StringFormatting
#add_taxon Bio::Nexus::TaxaBlock
#add_taxon Bio::Nexus::DataBlock
#add_token Bio::Nexus::GenericBlock
#add_tree Bio::Nexus::TreesBlock
#add_tree_name Bio::Nexus::TreesBlock
addindex_bdb Bio::FlatFileIndex::Indexer
addindex_flat Bio::FlatFileIndex::Indexer
#adjacency_matrix Bio::Tree
#adjacent_nodes Bio::Tree
#affiliations Bio::Reference
#aldh2 Bio::Shell::Demo
#alias_list Bio::KEGG::Keggtab
#aliases Bio::KEGG::Keggtab
#aliases Bio::KEGG::Keggtab::DB
#align Bio::MAFFT::Report
#align Bio::Spidey::Report::Hit
#align Bio::Sim4::Report::Hit
align Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
#align Bio::ClustalW::Report
#align_len Bio::Blat::Report::SegmentPair
#align_len Bio::Spidey::Report::SegmentPair
#align_len Bio::Blast::Report::Hsp
#align_len Bio::Sim4::Report::SegmentPair
#align_len Bio::Blast::Default::Report::HSP
align_with_cuts Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
#aligned_strands Bio::RestrictionEnzyme::DoubleStranded
#aligned_strands_with_cuts Bio::RestrictionEnzyme::DoubleStranded
#alignment Bio::ClustalW::Report
#alignment Bio::MAFFT::Report
#alignment Bio::Alignment::MultiFastaFormat
#alignment Bio::GCG::Msf
#alignment Bio::Phylip::PhylipFormat
#alignment_collect Bio::Alignment::EnumerableExtension
#alignment_collect Bio::Alignment::OriginalAlignment
#alignment_collect Bio::Alignment::HashExtension
#alignment_concat Bio::Alignment::HashExtension
#alignment_concat Bio::Alignment::EnumerableExtension
#alignment_length Bio::Alignment::EnumerableExtension
#alignment_length Bio::Phylip::PhylipFormat
#alignment_lstrip! Bio::Alignment::EnumerableExtension
#alignment_normalize! Bio::Alignment::EnumerableExtension
#alignment_rstrip! Bio::Alignment::EnumerableExtension
#alignment_site Bio::Alignment::EnumerableExtension
#alignment_slice Bio::Alignment::EnumerableExtension
#alignment_strip! Bio::Alignment::EnumerableExtension
#alignment_subseq Bio::Alignment::EnumerableExtension
#alignment_window Bio::Alignment::EnumerableExtension
alink Bio::DBGET
#all Bio::Shell::Demo
#all_hits Bio::Sim4::Report
#all_hits Bio::Spidey::Report
#all_reac Bio::KEGG::ENZYME
#alpha Bio::PAML::Codeml::ReportSingle
#alpha Bio::PAML::Codeml::Report
#alpha Bio::PAML::Codeml::Model
#alt Bio::KEGG::KGML::Reaction
#alt Bio::PhyloXML::Point
#alt_unit Bio::PhyloXML::Point
#altid Bio::FANTOM::MaXML::Sequence
#always_check Bio::FlatFileIndex::DataBank
#always_check_consistency Bio::FlatFileIndex
#always_check_consistency= Bio::FlatFileIndex
#analyzeParam Bio::DDBJ::REST::ClustalW
#analyzeParam Bio::DDBJ::REST::Mafft
#analyzeParamAsync Bio::DDBJ::REST::ClustalW
#analyzeParamAsync Bio::DDBJ::REST::Mafft
#analyzeSimple Bio::DDBJ::REST::Mafft
#analyzeSimple Bio::DDBJ::REST::ClustalW
#analyzeSimpleAsync Bio::DDBJ::REST::ClustalW
#analyzeSimpleAsync Bio::DDBJ::REST::Mafft
#ancestors Bio::Tree
#anisou Bio::PDB::Record::ATOM
#annotations Bio::FANTOM::MaXML::Sequence
#annotations Bio::PhyloXML::Sequence
#antisense Bio::SiRNA::Pair
#antisense_size Bio::SiRNA
#append Bio::Feature
#append Bio::Features
#append Bio::References
#append Bio::Pathway
#append Bio::Features::BackwardCompatibility
#append Bio::References::BackwardCompatibility
#append_hsp Bio::HMMER::Report::Hit
#applies_to Bio::PhyloXML::Property
#aqual Bio::Scf
#args Bio::PSORT::CGIDriver
array_to_string Bio::Nexus::Util
#ask_yes_or_no Bio::Shell::Core
#aspect Bio::GO::GeneAssociation
#assigned_by Bio::GO::GeneAssociation
#assoc Bio::Feature
#at_content Bio::Sequence::NA
#at_skew Bio::Sequence::NA
#atoms Bio::PDB::Residue
#atoms Bio::PDB::AtomFinder
#atrace Bio::SangerChromatogram
#attributes Bio::PhyloXML::Other
#attributes Bio::GFF::Record
#attributes_to_hash Bio::GFF::GFF2::Record
#au Bio::MEDLINE
#author Bio::AAindex
#author Bio::LITDB
#authority Bio::Taxonomy
#authors Bio::PDB
#authors Bio::MEDLINE
#authors Bio::Reference
auto Bio::FlatFile
#auto Bio::Sequence
auto Bio::Sequence
auto Bio::AAindex
#autodetect Bio::FlatFile
autodetect Bio::FlatFile
#autodetect Bio::FlatFile::AutoDetect
autodetect_file Bio::FlatFile
#autodetect_flatfile Bio::FlatFile::AutoDetect
autodetect_io Bio::FlatFile
autodetect_stream Bio::FlatFile
#average_length Bio::Lasergene
#ba Bio::TRANSFAC::MATRIX
#basecount Bio::GenBank
#bc Bio::TRANSFAC::GENE
#bc_type Bio::PhyloXML::BinaryCharacters
#bdb_open Bio::FlatFileIndex::DataBank
#bellman_ford Bio::Pathway
#bf Bio::TRANSFAC::MATRIX
#bf Bio::TRANSFAC::SITE
#bf Bio::TRANSFAC::CLASS
bfind Bio::DBGET
#bfs_shortest_path Bio::Pathway
#bgcolor Bio::KEGG::KGML::Graphics
#bgcolor Bio::KEGG::KGML::Entry
#bgcolor= Bio::KEGG::KGML::Entry
bget Bio::DBGET
#bibitem Bio::Reference
#bibtex Bio::Reference
#binary_characters Bio::PhyloXML::Node
binfo Bio::DBGET
#bioflat_dir Bio::Shell::Core
#bioroot Bio::KEGG::Keggtab
#bit_score Bio::Blast::Default::Report::Hit
#bit_score Bio::Blast::Report::Hit
#bit_score Bio::Blast::Report::Hsp
#bit_score Bio::Blast::Default::Report::HSP
#bit_score Bio::Fasta::Report::Hit
#blastall Bio::Blast
blink Bio::DBGET
#block_count Bio::Blat::Report::Hit
#block_it Bio::SiRNA::ShRNA
#block_sizes Bio::Blat::Report::Hit
#blocks Bio::Blat::Report::Hit
#blocksize Bio::Blat::Report::SegmentPair
#blue Bio::PhyloXML::BranchColor
#blunt? Bio::RestrictionEnzyme::DoubleStranded
bman Bio::DBGET
#bootstrap Bio::Tree::Node
#bootstrap_string Bio::Tree::Node
both_intron Bio::Sim4::Report::SegmentPair
#bottom_strand Bio::SiRNA::ShRNA
#bottom_strand_sequences Bio::Lasergene
#branch_length_unit Bio::PhyloXML::Tree
#breadth_first_search Bio::Pathway
bref Bio::DBGET
#bs Bio::TRANSFAC::FACTOR
#bs Bio::TRANSFAC::GENE
btab Bio::DBGET
btit Bio::DBGET
#c Bio::RestrictionEnzyme::Range::SequenceRange::Bin
#c2s Bio::Sequence::NA::MidiTrack
#c_cut_left Bio::RestrictionEnzyme::Range::VerticalCutRange
#c_cut_left Bio::RestrictionEnzyme::Range::HorizontalCutRange
#c_cut_right Bio::RestrictionEnzyme::Range::VerticalCutRange
#c_cut_right Bio::RestrictionEnzyme::Range::HorizontalCutRange
#c_left Bio::RestrictionEnzyme::Fragment
#c_left Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#c_left Bio::RestrictionEnzyme::Range::SequenceRange
#c_right Bio::RestrictionEnzyme::Range::SequenceRange
#c_right Bio::RestrictionEnzyme::Fragment
#c_right Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#cache Bio::Shell::Ghost
#cache_all Bio::FlatFileIndex::FileIDs
calc_checksum Bio::GCG::Seq
calculatePlane Bio::PDB::Utils
#call Bio::Command::Tmpdir::Remover
call_command Bio::Command
call_command_fork Bio::Command
call_command_open3 Bio::Command
call_command_popen Bio::Command
#carat Bio::Location
#category Bio::DAS::TYPE
#cc Bio::EMBL
#cc Bio::SPTR
#cc Bio::TRANSFAC
#cc Bio::PROSITE
#cd Bio::TRANSFAC::CELL
#cdna_rep_h_invitational Bio::Hinv::HitDefinition
#cdna_splicing_isoform_curation Bio::Hinv::HitDefinition
#cds_start Bio::FANTOM::MaXML::Annotations
#cds_stop Bio::FANTOM::MaXML::Annotations
#cdsfeatures Bio::SQL::Sequence
#cell Bio::Reference
#centreOfGravity Bio::PDB::Utils
#chain Bio::PDB::Residue
#chain_id Bio::PDB::Chain
#chains Bio::PDB::ChainFinder
#chains Bio::PDB::Model
#characters Bio::ContingencyTable
#check Bio::FlatFileIndex::FileID
#check_all Bio::FlatFileIndex::FileIDs
#check_consistency Bio::FlatFileIndex::DataBank
#check_consistency Bio::FlatFileIndex
#check_marshal Bio::Shell::Ghost
#check_options Bio::Meme::Mast
#check_ruby_version Bio::Shell::Setup
#checksum Bio::GCG::Seq
#checksum Bio::GCG::Msf
#chemistry Bio::Abif
#chi_square Bio::ContingencyTable
#chi_square_element Bio::ContingencyTable
#child_nodes Bio::KEGG::Keggtab
#children Bio::Tree
#children Bio::PhyloXML::Other
chose_sort_proc Bio::FlatFileIndex::Indexer
#chromatogram_type Bio::SangerChromatogram
#chromosome Bio::KEGG::GENES
#chromosomes Bio::KEGG::GENOME
#circular Bio::GenBank::Locus
#circular Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#circular Bio::GenBank
#circular Bio::GenPept
#circular Bio::GenPept::Locus
#cl Bio::TRANSFAC::CLASS
#cl Bio::TRANSFAC::FACTOR
#clade_relations Bio::PhyloXML::Tree
#classes Bio::PAML::Codeml::Model
#classes Bio::KEGG::ENZYME
#classification Bio::PDB
#classification Bio::GenBank
#classification Bio::Sequence
#clear Bio::Tree
#clear_node Bio::Tree
#clear_relations! Bio::Pathway
#cleavage_site_prediction Bio::TargetP::Report
#clique Bio::Pathway
#cliquishness Bio::Pathway
#cloneids Bio::FANTOM::MaXML::Sequences
#close Bio::FlatFile
#close Bio::FlatFileIndex
#close Bio::FlatFileIndex::DataBank
#close Bio::PhyloXML::Parser
#close Bio::FlatFileIndex::BDBwrapper
#close Bio::FlatFileIndex::BDB_1::BDBMappingFile
#close Bio::FlatFileIndex::FileID
#close Bio::FlatFile::BufferedInputStream
#close Bio::FlatFileIndex::Flat_1::FlatMappingFile
#close Bio::FlatFileIndex::Template::NameSpace
#close! Bio::Command::Tmpdir
#close_all Bio::FlatFileIndex::FileIDs
#close_all Bio::FlatFileIndex::NameSpaces
#close_flatfile Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#close_history Bio::Shell::Ghost
#closed? Bio::PhyloXML::Parser
#closed? Bio::FlatFileIndex
#closing_splash Bio::Shell::Ghost
#cmd Bio::Meme::Mast
#cn Bio::TRANSFAC::FACTOR
#co Bio::TRANSFAC::GENE
#code Bio::Taxonomy
#code Bio::GFF::GFF3::Record::Gap::Code
#codes Bio::Sequence::AA
#codon_usage Bio::Sequence::NA
#codon_usage Bio::KEGG::GENES
#cofactors Bio::KEGG::ENZYME
#collect! Bio::Alignment::OriginalAlignment
#collect_each_site Bio::Alignment::EnumerableExtension
#collect_edge! Bio::Tree
#collect_node! Bio::Tree
#color Bio::PhyloXML::Node
#colors Bio::Shell::Core
colors Bio::ColorScheme::Simple
colors Bio::ColorScheme::Score
#cols Bio::AAindex2
#column_index Bio::SOFT::Table::Header
#column_sum Bio::ContingencyTable
#column_sum_all Bio::ContingencyTable
#columns Bio::Blat::Report
#command Bio::MAFFT
#command Bio::Alignment::FactoryTemplate::Simple
#command Bio::Sim4
#command Bio::PAML::Common
#command Bio::ClustalW
#commands BiorubyController
#comment Bio::KEGG::DRUG
#comment Bio::GFF::GFF2::Record
#comment Bio::GFF::Record
#comment Bio::KEGG::COMPOUND
#comment Bio::KEGG::ENZYME
#comment Bio::KEGG::GENOME
#comment Bio::AAindex
#comment Bio::FastaFormat
#comment Bio::NCBIDB::Common
#comment Bio::KEGG::GLYCAN
#comment= Bio::SQL::Sequence
#comment_only? Bio::GFF::GFF2::Record
#comments Bio::Reference
#comments Bio::Lasergene
#comments Bio::Sequence
#comments Bio::SQL::Sequence
#comments Bio::GFF::GFF2::Record
#comments Bio::GFF::Record
#comments Bio::Scf
#comments= Bio::GFF::GFF2::Record
#comments= Bio::GFF::Record
#common_name Bio::NCBIDB::Common
#common_names Bio::Taxonomy
#common_subgraph Bio::Pathway
#compact Bio::Alignment::OriginalAlignment
#compact! Bio::Alignment::OriginalAlignment
#compcheck Bio::GCG::Msf
#complement Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
#complement Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
#complement Bio::RestrictionEnzyme::Range::SequenceRange::Fragments::DisplayFragment
#complement Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
#complement Bio::RestrictionEnzyme::Fragments
#complement Bio::RestrictionEnzyme::DoubleStranded
#complement Bio::RestrictionEnzyme::Fragment
#complement Bio::RestrictionEnzyme::DoubleStranded::CutLocations
#complement Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#complement Bio::SangerChromatogram
#complement Bio::Location
#complement! Bio::SangerChromatogram
#complement? Bio::Sim4::Report::Hit
#complement? Bio::Spidey::Report::Hit
#complement_to_array_index Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
#components Bio::KEGG::KGML::Entry
#composition Bio::Sequence::Common
#composition Bio::KEGG::GLYCAN
#compounds Bio::KEGG::GLYCAN
#compounds_as_hash Bio::KEGG::MODULE
#compounds_as_hash Bio::KEGG::PATHWAY
#compounds_as_strings Bio::KEGG::PATHWAY
#compounds_as_strings Bio::KEGG::MODULE
#concat Bio::Sequence::Common
#concat Bio::RestrictionEnzyme::DenseIntArray
#concat Bio::RestrictionEnzyme::SortedNumArray
#concat Bio::Alignment::OriginalAlignment
#concat Bio::Tree
#conect Bio::PDB::ChemicalComponent
#confidence Bio::PhyloXML::CladeRelation
#confidence Bio::PhyloXML::Events
#confidence Bio::PhyloXML::ProteinDomain
#confidence Bio::PhyloXML::Annotation
#confidences Bio::PhyloXML::Node
#confidences Bio::PhyloXML::Tree
#config Bio::Meme::Mast
#config Bio::Shell::Ghost
#config_color Bio::Shell::Ghost
#config_echo Bio::Shell::Ghost
#config_file Bio::Shell::Core
#config_message Bio::Shell::Ghost
#config_pager Bio::Shell::Ghost
#config_show Bio::Shell::Ghost
#config_splash Bio::Shell::Ghost
#configure Bio::Shell::Ghost
#consensus_each_site Bio::Alignment::EnumerableExtension
#consensus_iupac Bio::Alignment::SiteMethods
#consensus_iupac Bio::Alignment::EnumerableExtension
#consensus_string Bio::Alignment::SiteMethods
#consensus_string Bio::Alignment::EnumerableExtension
#contains_marker? Bio::Map::ActsLikeMap
#contig_length Bio::Lasergene
#contingency_coefficient Bio::ContingencyTable
#continue? Bio::PDB::Record
continue? Bio::PDB::Record
#control_avg Bio::KEGG::EXPRESSION
#control_sd Bio::KEGG::EXPRESSION
#control_var Bio::KEGG::EXPRESSION
#converged? Bio::Blast::Default::Report::Iteration
#converged? Bio::Blast::Default::Report
convert Bio::TogoWS::REST
#convert Bio::TogoWS::REST
#convert_match Bio::Alignment::EnumerableExtension
#convert_nothing Bio::Sequence::QualityScore::Converter
#convert_scores_from_phred_to_solexa Bio::Sequence::QualityScore::Converter
#convert_scores_from_solexa_to_phred Bio::Sequence::QualityScore::Converter
convert_scores_to_phred Bio::Sequence::QualityScore::Solexa
convert_scores_to_solexa Bio::Sequence::QualityScore::Phred
convert_to_xyz Bio::PDB::Utils
#convert_unmatch Bio::Alignment::EnumerableExtension
#coords Bio::KEGG::KGML::Graphics
copy Bio::CodonTable
#correlation_coefficient Bio::AAindex1
#count Bio::DAS::TYPE
#count Bio::NCBI::REST::ESearch::Methods
#countBasePair Bio::DDBJ::REST::DDBJ
#cp Bio::TRANSFAC::FACTOR
#cqual Bio::Scf
#crc64 Bio::Iprscan::Report::Match
#crc64 Bio::Iprscan::Report
create Bio::FlatFileIndex::Flat_1::Record
#create_action_at Bio::RestrictionEnzyme::DoubleStranded
create_config_file Bio::PAML::Codeml
create_control_file Bio::PAML::Codeml
create_definition_hash Bio::PDB::Record
#create_flat_dir Bio::Shell::Ghost
#create_real_dir Bio::Shell::Ghost
#create_save_dir Bio::Shell::Ghost
#create_save_dir_ask Bio::Shell::Ghost
#csline Bio::HMMER::Report::Hsp
#cterm Bio::PTS1::Report
#ctrace Bio::SangerChromatogram
#cu_list Bio::KEGG::GENES
#current Bio::Reference
#cut Bio::RestrictionEnzyme::Analysis
cut Bio::RestrictionEnzyme
cut Bio::RestrictionEnzyme::Analysis
#cut_locations Bio::RestrictionEnzyme::DoubleStranded
#cut_locations Bio::RestrictionEnzyme::SingleStrand
#cut_locations_in_enzyme_notation Bio::RestrictionEnzyme::SingleStrand
#cut_locations_in_enzyme_notation Bio::RestrictionEnzyme::DoubleStranded
#cut_ranges Bio::RestrictionEnzyme::Range::SequenceRange
#cut_symbol Bio::RestrictionEnzyme::CutSymbol
cut_symbol Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
cut_symbol= Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
#cut_with_enzyme Bio::Sequence::NA
cut_without_permutations Bio::RestrictionEnzyme::Analysis
#cut_without_permutations Bio::RestrictionEnzyme::Analysis
#cutoff Bio::TargetP::Report
#dN_dS Bio::PAML::Codeml::PositiveSite
#data Bio::FastaNumericFormat
#data Bio::NBRF
#data Bio::PDB
#data Bio::Blat::Report::Hit
#data Bio::Abif::DirectoryEntry
#data Bio::GFF::GFF2::MetaData
#data Bio::MAFFT::Report
#data Bio::PDB::ChemicalComponent
#data Bio::Abif
#data Bio::Fasta::Report::Hit::Query
#data Bio::FastaFormat
#data_class Bio::EMBL
#data_class Bio::Sequence
#data_dir Bio::Shell::Core
#data_offset Bio::Abif::DirectoryEntry
#data_size Bio::Abif::DirectoryEntry
#data_source Bio::KEGG::GENOME
#data_source Bio::FANTOM::MaXML::Annotations
#data_source_coverage Bio::Hinv::HitDefinition
#data_source_db_reference_protein_motif_id Bio::Hinv::HitDefinition
#data_source_homologous_species Bio::Hinv::HitDefinition
#data_source_identity Bio::Hinv::HitDefinition
#data_source_similarity_category Bio::Hinv::HitDefinition
#data_stdout Bio::Alignment::FactoryTemplate::Simple
#data_stdout Bio::PAML::Common
#data_stdout Bio::MAFFT
#data_stdout Bio::ClustalW
#database Bio::SQL::Sequence
#database Bio::Fetch
#database Bio::Blast::Fastacmd
#database Bio::SOFT
#database Bio::Registry::DB
#database Bio::KEGG::Keggtab
#database Bio::Sequence::DBLink
#database Bio::Blast::Default::Report::Iteration
#database Bio::Sim4
#database Bio::Blast::Default::Report::F0dbstat
#database_desc Bio::SQL::Sequence
#database_description Bio::Blast::Remote::Information
#databases Bio::Blast::Remote::Information
#databases Bio::Registry
#databases Bio::Fetch
#dataset Bio::SOFT
#datasrc Bio::FANTOM::MaXML::Annotation
#datatype Bio::PhyloXML::Property
#date Bio::GenPept
#date Bio::Iprscan::Report::Match
#date Bio::PhyloXML::Tree
#date Bio::GCG::Seq
#date Bio::GenBank::Locus
#date Bio::GO::GeneAssociation
#date Bio::PhyloXML::Node
#date Bio::GenBank
#date Bio::GCG::Msf
#date Bio::GenPept::Locus
#date_created Bio::EMBL
#date_created Bio::Sequence
#date_modified Bio::GenBank
#date_modified Bio::EMBL
#date_modified Bio::Sequence
#date_run Bio::Genscan::Report
#db Bio::Blast::WU::Report
#db Bio::Blast
#db Bio::Blast::Report
#db Bio::GO::GeneAssociation
#db Bio::Blast::Default::Report
#db Bio::Fasta
#db_by_abbrev Bio::KEGG::Keggtab
#db_ids Bio::GO::External2go
#db_len Bio::Blast::Default::Report::F0dbstat
#db_len Bio::Blast::Default::Report
#db_len Bio::Blast::Report
#db_len Bio::Blast::Bl2seq::Report::F0dbstat
#db_len Bio::Blast::Default::Report::Iteration
#db_names Bio::KEGG::Keggtab
#db_num Bio::Blast::Report
#db_num Bio::Blast::Bl2seq::Report::F0dbstat
#db_num Bio::Blast::Default::Report::F0dbstat
#db_num Bio::Blast::Default::Report
#db_num Bio::Blast::Default::Report::Iteration
#db_object_id Bio::GO::GeneAssociation
#db_object_name Bio::GO::GeneAssociation
#db_object_symbol Bio::GO::GeneAssociation
#db_object_synonym Bio::GO::GeneAssociation
#db_object_type Bio::GO::GeneAssociation
#db_path Bio::KEGG::Keggtab
#db_path_by_abbrev Bio::KEGG::Keggtab
#db_reference Bio::GO::GeneAssociation
#dbclass Bio::FlatFile
#dbclass Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#dbclasses Bio::FlatFile::AutoDetect::RuleRegexp
#dbclasses Bio::FlatFile::AutoDetect::RuleTemplate
#dbclasses Bio::FlatFile::AutoDetect::RuleProc
dbget Bio::DBGET
#dblinks Bio::EMBL
#dblinks Bio::AAindex
#dblinks Bio::Sequence
#dblinks_as_hash Bio::KEGG::GLYCAN
#dblinks_as_hash Bio::KEGG::COMPOUND
#dblinks_as_hash Bio::KEGG::PATHWAY
#dblinks_as_hash Bio::KEGG::ENZYME
#dblinks_as_hash Bio::KEGG::DRUG
#dblinks_as_hash Bio::KEGG::GENES
#dblinks_as_hash Bio::KEGG::Common::DblinksAsHash
#dblinks_as_hash Bio::KEGG::ORTHOLOGY
#dblinks_as_strings Bio::KEGG::COMPOUND
#dblinks_as_strings Bio::KEGG::GENES
#dblinks_as_strings Bio::KEGG::ORTHOLOGY
#dblinks_as_strings Bio::KEGG::ENZYME
#dblinks_as_strings Bio::KEGG::GLYCAN
#dblinks_as_strings Bio::KEGG::DRUG
#dblinks_as_strings Bio::KEGG::PATHWAY
#dbname Bio::FlatFileIndex::Template::NameSpace
#dbname Bio::FlatFileIndex::DataBank
#dbref Bio::PDB
#dbs Bio::GO::External2go
#dbsource Bio::GenPept
ddbj Bio::Blast::Remote
#de Bio::TRANSFAC::SITE
#de Bio::TRANSFAC::MATRIX
#de Bio::TRANSFAC::GENE
#de Bio::EMBLDB::Common
#de Bio::PROSITE
#debug Bio::TogoWS::REST
def_rec Bio::PDB::Record
default Bio::FlatFile::AutoDetect
default= Bio::FlatFile::AutoDetect
default_email Bio::NCBI
default_email= Bio::NCBI
#default_namespaces Bio::FlatFileIndex
#default_namespaces= Bio::FlatFileIndex
default_parser Bio::PSORT::PSORT2::Report
default_parser Bio::PSORT::PSORT1::Report
default_tool Bio::NCBI
default_tool= Bio::NCBI
#definition Bio::KEGG::MODULE
#definition Bio::KEGG::GENES
#definition Bio::Spidey::Report::SeqDesc
#definition Bio::Fasta::Report::Program
#definition Bio::NBRF
#definition Bio::CodonTable
#definition Bio::KEGG::REACTION
#definition Bio::Fasta::Report::Hit
#definition Bio::NCBIDB::Common
#definition Bio::PSORT::PSORT2::Report
#definition Bio::KEGG::ORTHOLOGY
#definition Bio::GCG::Seq
#definition Bio::AAindex
#definition Bio::Sim4::Report::SeqDesc
#definition Bio::KEGG::GENOME
#definition Bio::Blast::Default::Report::Hit
#definition Bio::Fasta::Report::Hit::Query
#definition Bio::Fastq
#definition Bio::PDB
#definition Bio::FastaFormat
#definition Bio::Blast::Report::Hit
#definition Bio::Sequence
#delete Bio::RestrictionEnzyme::DenseIntArray
#delete Bio::RestrictionEnzyme::SortedNumArray
#delete Bio::SQL::Sequence
#delete Bio::Blast::NCBIOptions
#delete Bio::Alignment::OriginalAlignment
#delete Bio::Pathway
#delete_attribute Bio::GFF::GFF2::Record
#delete_attributes Bio::GFF::GFF2::Record
delete_entry_accession Bio::SQL
delete_entry_id Bio::SQL
#delimiter Bio::FlatFile::Splitter::Default
#delimiter_overrun Bio::FlatFile::Splitter::Default
#density Bio::Blast::Report::Hsp
#depth_first_search Bio::Pathway
#desc Bio::PhyloXML::Uri
#desc Bio::PhyloXML::Date
#desc Bio::PhyloXML::Distribution
#desc Bio::PhyloXML::Annotation
#desc Bio::PhyloXML::Reference
#descendents Bio::Tree
#descr Bio::PAML::Codeml::PositiveSites
#descr Bio::PAML::Codeml::Report
#description Bio::Iprscan::Report::Match
#description Bio::SQL::Sequence
#description Bio::PhyloXML::Tree
#description Bio::HMMER::Report::Hit
#description Bio::DAS::SEGMENT
#description Bio::DAS::DSN
#description Bio::GCG::Msf
#description Bio::FastaDefline
#description Bio::KEGG::PATHWAY
#description= Bio::SQL::Sequence
#description_href Bio::DAS::DSN
#descriptions Bio::FastaDefline
#design Bio::SiRNA::ShRNA
#design Bio::SiRNA
#dfs_topological_sort Bio::Pathway
dihedral_angle Bio::PDB::Utils
#dijkstra Bio::Pathway
#directed Bio::Pathway
#directed? Bio::Pathway
#direction Bio::Fasta::Report::Hit
#direction Bio::Sim4::Report::SegmentPair
#directive Bio::GFF::GFF2::MetaData
#disease Bio::KEGG::GENOME
#diseases Bio::KEGG::ENZYME
#diseases_as_hash Bio::KEGG::PATHWAY
#diseases_as_strings Bio::KEGG::PATHWAY
#distance Bio::PDB::Coordinate
#distance Bio::PhyloXML::SequenceRelation
#distance Bio::PhyloXML::CladeRelation
distance Bio::PDB::Utils
#distance Bio::Tree
#distance Bio::Tree::Edge
#distance_matrix Bio::Tree
#distance_string Bio::Tree::Edge
#distributions Bio::PhyloXML::Node
divent Bio::PSORT::PSORT2::Report
#division Bio::Sequence
#division Bio::SQL::Sequence
#division Bio::KEGG::GENES
#division Bio::EMBL
#division Bio::GenPept
#division Bio::PROSITE
#division Bio::GenBank
#division Bio::GenPept::Locus
#division Bio::GenBank::Locus
#division= Bio::SQL::Sequence
#dna Bio::Sequence::NA
#dna Bio::DAS
#dna! Bio::Sequence::NA
#do_align Bio::Alignment::OriginalAlignment
#do_parse Bio::PDB::Record::ATOM
#do_parse Bio::PDB::Record
#doi Bio::Reference
#doi Bio::PhyloXML::Reference
#doi Bio::MEDLINE
#domain Bio::HMMER::Report::Hsp
#domain_architecture Bio::PhyloXML::Sequence
#domain_top_hits Bio::HMMER::Report
#domains Bio::PhyloXML::DomainArchitecture
#donor_score Bio::Genscan::Report::Exon
#down_regulated Bio::KEGG::EXPRESSION
#dp Bio::MEDLINE
#dr Bio::SPTR
#dr Bio::PROSITE
#dr Bio::TRANSFAC::FACTOR
#dr Bio::TRANSFAC::SITE
#dr Bio::EMBLDB::Common
#dr Bio::TRANSFAC::CLASS
#dt Bio::PROSITE
#dt Bio::TRANSFAC
#dt Bio::SPTR
#dt Bio::EMBL
#dump_list Bio::Pathway
#dump_matrix Bio::Pathway
#dump_parameters Bio::PAML::Common
#dup Bio::Alignment::OriginalAlignment
#duplications Bio::PhyloXML::Events
#dye_mobility Bio::SangerChromatogram
#each Bio::CodonTable
#each Bio::Locations
#each Bio::Blast::Report::Iteration
#each Bio::FlatFileIndex::Flat_1::FlatMappingFile
#each Bio::RestrictionEnzyme::SortedNumArray
#each Bio::Sim4::Report::Hit
#each Bio::Meme::Mast::Report
#each Bio::Spidey::Report::Hit
#each Bio::HMMER::Report
#each Bio::HMMER::Report::Hit
#each Bio::Fasta::Report
#each Bio::Feature
#each Bio::Features
#each Bio::PDB::Residue
#each Bio::REBASE
#each Bio::Blast::Default::Report::Iteration
#each Bio::FANTOM::MaXML::Annotations
#each Bio::DAS::ENTRY_POINT
#each Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#each Bio::Blast::Report::Hit
#each Bio::RestrictionEnzyme::DenseIntArray
#each Bio::PDB::Chain
#each Bio::PhyloXML::Parser
#each Bio::FANTOM::MaXML::Sequences
#each Bio::PDB
#each Bio::FlatFileIndex::FileIDs
#each Bio::References
#each Bio::PDB::Model
#each Bio::Blast::Default::Report::Hit
#each Bio::FastaNumericFormat
#each Bio::Alignment::OriginalAlignment
#each Bio::Blat::Report::Hit
#each_atom Bio::PDB::AtomFinder
#each_cds Bio::EMBL
#each_cds Bio::GenBank
#each_chain Bio::PDB::ChainFinder
#each_edge Bio::Tree
#each_edge_in_path Bio::Tree
#each_entry Bio::FlatFile
#each_entry Bio::Blast::Fastacmd
#each_files Bio::FlatFileIndex::NameSpaces
#each_gene Bio::EMBL
#each_gene Bio::GenBank
#each_hetatm Bio::PDB::HetatmFinder
#each_heterogen Bio::PDB::Chain
#each_heterogen Bio::PDB::HeterogenFinder
#each_hit Bio::Blat::Report
#each_hit Bio::Blast::Report
#each_hit Bio::Spidey::Report
#each_hit Bio::Sim4::Report
#each_hit Bio::Blast::Default::Report
#each_iteration Bio::Blast::Report
#each_iteration Bio::Blast::Default::Report
#each_names Bio::FlatFileIndex::NameSpaces
#each_node Bio::Tree
#each_out_edge Bio::Tree
#each_pair Bio::Alignment::OriginalAlignment
#each_residue Bio::PDB::ResidueFinder
#each_rule Bio::FlatFile::AutoDetect
#each_seq Bio::Alignment::EnumerableExtension
#each_seq Bio::Alignment::HashExtension
#each_seq Bio::Alignment::ArrayExtension
#each_site Bio::Alignment::EnumerableExtension
#each_site_step Bio::Alignment::EnumerableExtension
#each_symbol Bio::PDB::Record
#each_window Bio::Alignment::EnumerableExtension
#each_with_index Bio::FlatFileIndex::FileIDs
#ec_number Bio::Tree::Node
#eclinks Bio::KEGG::GENES
#edge Bio::Relation
#edge Bio::KEGG::KGML::Relation
#edges Bio::Pathway
#edges Bio::Tree
efetch Bio::PubMed
efetch Bio::NCBI::REST
#efetch Bio::NCBI::REST
#efetch Bio::PubMed
#eff_space Bio::Blast::Default::Report::Iteration
#eff_space Bio::Blast::Report
#eff_space Bio::Blast::Default::Report::F0dbstat
#eff_space Bio::Blast::Default::Report
#einfo Bio::NCBI::REST
einfo Bio::NCBI::REST
#el Bio::TRANSFAC::SITE
#elem Bio::FANTOM::MaXML
#element_name Bio::PhyloXML::Other
#element_size Bio::Abif::DirectoryEntry
#element_type Bio::Abif::DirectoryEntry
elements Bio::PDB::Coordinate
#elements Bio::FlatFile::AutoDetect
#embl Bio::Reference
#embl_dr Bio::SPTR
#embl_gb_record_number Bio::Reference
#encode Bio::Sequence::NA::MidiTrack
#end Bio::Hinv::KeywordSearch
#end Bio::GFF::GFF3::Record::Target
#end Bio::GFF::GFF3::SequenceRegion
#end Bio::GFF::Record
#end Bio::Blat::Report::SeqDesc
#end_pos Bio::Meme::Motif
#endnote Bio::Reference
entret Bio::EMBOSS
#entrez_query Bio::Blast::Report
#entries Bio::KEGG::KGML
#entries Bio::Alignment::MultiFastaFormat
#entropy Bio::Blast::Default::Report::Iteration
#entropy Bio::Blast::Report
#entropy Bio::Blast::Default::Report
#entry Bio::FlatFile::Splitter::Template
#entry Bio::EMBL
#entry Bio::Shell::Demo
#entry Bio::FastaFormat
#entry Bio::Blast::Report::BlastXmlSplitter
#entry Bio::NBRF
#entry Bio::FlatFile
#entry Bio::KEGG::ENZYME
#entry Bio::KEGG::GENES
#entry Bio::SQL::Sequence
#entry Bio::TogoWS::REST
entry Bio::TogoWS::REST
#entry1 Bio::KEGG::KGML::Relation
#entry2 Bio::KEGG::KGML::Relation
entry_database_list Bio::TogoWS::REST
#entry_database_list Bio::TogoWS::REST
#entry_ended_pos Bio::FlatFile
#entry_ended_pos Bio::FlatFile::Splitter::Template
#entry_ended_pos Bio::Blast::Report::BlastXmlSplitter
#entry_id Bio::KEGG::MODULE
#entry_id Bio::KEGG::GENES
#entry_id Bio::PSORT::PSORT2::Report
#entry_id Bio::GenPept
#entry_id Bio::Sequence
#entry_id Bio::KEGG::DRUG
#entry_id Bio::Sim4::Report::SeqDesc
#entry_id Bio::TMHMM::Report
#entry_id Bio::PSORT::PSORT1::Report
#entry_id Bio::LITDB
#entry_id Bio::Fastq
#entry_id Bio::KEGG::COMPOUND
#entry_id Bio::FastaFormat
#entry_id Bio::PDB::ChemicalComponent
#entry_id Bio::PDB
#entry_id Bio::KEGG::GENOME
#entry_id Bio::KEGG::PATHWAY
#entry_id Bio::NBRF
#entry_id Bio::DAS::GROUP
#entry_id Bio::GenBank
#entry_id Bio::DAS::TARGET
#entry_id Bio::DAS::FEATURE
#entry_id Bio::DAS::TYPE
#entry_id Bio::DAS::SEQUENCE
#entry_id Bio::DAS::DNA
#entry_id Bio::KEGG::GLYCAN
#entry_id Bio::DAS::SEGMENT
#entry_id Bio::KEGG::ORTHOLOGY
#entry_id Bio::Spidey::Report::SeqDesc
#entry_id Bio::GenBank::Locus
#entry_id Bio::Lasergene
#entry_id Bio::GCG::Seq
#entry_id Bio::FastaDefline
#entry_id Bio::DB
#entry_id Bio::KEGG::REACTION
#entry_id Bio::FANTOM::MaXML::Annotation
#entry_id Bio::FANTOM::MaXML
#entry_id Bio::SOSUI::Report
#entry_id Bio::GCG::Msf
#entry_id Bio::PTS1::Report
#entry_id Bio::AAindex
#entry_id Bio::GenPept::Locus
#entry_id Bio::Fasta::Report::Hit::Query
#entry_id Bio::KEGG::ENZYME
#entry_id Bio::TMHMM::TMH
#entry_id Bio::SPTR
#entry_overrun Bio::Blast::Default::Report
#entry_overrun Bio::Fastq
#entry_overrun Bio::FastaFormat
#entry_overrun Bio::Fasta::Report
#entry_overrun Bio::NBRF
#entry_overrun Bio::Newick
#entry_overrun Bio::Spidey::Report
#entry_pos_flag Bio::FlatFile::Splitter::Template
#entry_pos_flag Bio::FlatFile
#entry_pos_flag= Bio::FlatFile
#entry_raw Bio::FlatFile
#entry_start_pos Bio::Blast::Report::BlastXmlSplitter
#entry_start_pos Bio::FlatFile
#entry_start_pos Bio::FlatFile::Splitter::Template
#entry_version Bio::Sequence
#entry_version Bio::EMBL
enzyme_name? Bio::RestrictionEnzyme
#enzyme_name? Bio::REBASE
#enzymes Bio::KEGG::COMPOUND
#enzymes Bio::KEGG::REACTION
#enzymes Bio::KEGG::GLYCAN
#enzymes Bio::REBASE
#enzymes_as_strings Bio::KEGG::PATHWAY
#eof? Bio::FlatFile
#eof? Bio::FlatFile::BufferedInputStream
#equals? Bio::Locations
#equation Bio::KEGG::REACTION
#error_probabilities Bio::Sequence
#error_probabilities Bio::Fastq
#errorlog Bio::ClustalW
#errorlog Bio::FlatFileIndex::Indexer::Parser::TemplateParser
escape_shell Bio::Command
escape_shell_unix Bio::Command
escape_shell_windows Bio::Command
#escaped_cut_symbol Bio::RestrictionEnzyme::CutSymbol
escaped_cut_symbol Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
esearch Bio::NCBI::REST
#esearch Bio::NCBI::REST
esearch Bio::PubMed
#esearch Bio::PubMed
#esearch_count Bio::NCBI::REST
esearch_count Bio::NCBI::REST
#est Bio::NCBI::REST::ESearch::Methods
establish_connection Bio::SQL
#evaluate BiorubyController
#evalue Bio::Blast::Default::Report::HSP
#evalue Bio::Fasta::Report::Hit
#evalue Bio::Blast::Default::Report::Hit
#evalue Bio::Iprscan::Report::Match
#evalue Bio::Blast::Report::Hit
#evalue Bio::HMMER::Report::Hit
#evalue Bio::HMMER::Report::Hsp
#evalue Bio::Blast::Report::Hsp
#events Bio::Tree::Node
#events Bio::PhyloXML::Node
#evidence Bio::GO::GeneAssociation
#evidence Bio::PhyloXML::Annotation
#evidence Bio::FANTOM::MaXML::Annotations
#exec Bio::EMBOSS
#exec Bio::PSORT::PSORT2
#exec Bio::PTS1
#exec Bio::PSORT::PSORT1
#exec Bio::PSORT::CGIDriver
#exec_ddbj Bio::Blast::Remote::DDBJ
#exec_local Bio::Sim4
#exists? Bio::DB
exists_accession Bio::SQL
exists_database Bio::SQL
#exit_code Bio::Blast::WU::Report
#exit_code_message Bio::Blast::WU::Report
#exit_status Bio::ClustalW
#exit_status Bio::MAFFT
#exit_status Bio::Alignment::FactoryTemplate::Simple
#exit_status Bio::PAML::Common
#exon_type Bio::Genscan::Report::Exon
#exon_type_long Bio::Genscan::Report::Exon
#exons Bio::Sim4::Report::Hit
#exons Bio::Spidey::Report::Hit
#exons Bio::Genscan::Report::Gene
#exp_aas_in_tmhs Bio::TMHMM::Report
#exp_first_60aa Bio::TMHMM::Report
#expect Bio::Blast::Report
#expect Bio::Blast::Default::Report::F0dbstat
#expect Bio::Blast::WU::Report
#expect Bio::Blast::Default::Report
#expect Bio::Blast::Default::Report::Iteration
#expected Bio::ContingencyTable
#export_tsv Bio::FlatFileIndex::Flat_1::FlatMappingFile
#exportview Bio::Ensembl
exportview Bio::Ensembl::Base
external_merge_proc Bio::FlatFileIndex::Flat_1::FlatMappingFile
external_merge_sort_proc Bio::FlatFileIndex::Flat_1::FlatMappingFile
external_sort_proc Bio::FlatFileIndex::Flat_1::FlatMappingFile
#extractPosition Bio::DDBJ::REST::Blast
#extract_biosequence Bio::PhyloXML::Node
extract_key Bio::Alignment::OriginalPrivate
extract_seq Bio::Alignment::OriginalPrivate
#f0dbstat Bio::Blast::Default::Report::F0dbstat
#f0params Bio::Blast::Default::Report::F0dbstat
#fa Bio::TRANSFAC::FACTOR
#false_neg Bio::PROSITE
#false_pos Bio::PROSITE
#false_positive_hits Bio::PROSITE
#false_positive_sequences Bio::PROSITE
#fastacmd Bio::Blast::Fastacmd
#fatal_errors Bio::Blast::WU::Report
#feature Bio::Feature
#feature Bio::GFF::Record
#feature= Bio::SQL::Sequence
#features Bio::Sequence
#features Bio::Features
#features Bio::PSORT::PSORT2::Report
#features Bio::Features::BackwardCompatibility
#features Bio::DAS::SEGMENT
#features Bio::DAS
#features Bio::SQL::Sequence
#features Bio::NCBIDB::Common
#fetch Bio::Fetch
#fetch Bio::Blast::Fastacmd
#fetch Bio::DB
fetch_accession Bio::SQL
fetch_id Bio::SQL
#ff Bio::TRANSFAC::FACTOR
fftns Bio::MAFFT
fftnsi Bio::MAFFT
#fgcolor Bio::KEGG::KGML::Entry
#fgcolor Bio::KEGG::KGML::Graphics
#fgcolor= Bio::KEGG::KGML::Entry
#fh Bio::EMBL
#field Bio::LITDB
#file Bio::FlatFileIndex::Template::NameSpace
#fileid Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#fileids Bio::FlatFileIndex::DataBank
#filename Bio::FlatFileIndex::Template::NameSpace
#filename Bio::FlatFileIndex::FileID
#filename Bio::Sim4::Report::SeqDesc
#filename Bio::FlatFileIndex::BDBwrapper
#filename Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
filename Bio::FlatFileIndex::DataBank
#filename Bio::FlatFileIndex::Flat_1::FlatMappingFile
#filename Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
#filename Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
#filename Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
#filename Bio::FlatFileIndex::BDB_1::BDBMappingFile
#filenames Bio::FlatFileIndex::FileIDs
#filesize Bio::FlatFileIndex::FileID
#fill String
#filter Bio::Blast::Report
#filter Bio::Blast
#final_result Bio::PSORT::PSORT1::Report
#find_atom Bio::PDB::AtomFinder
#find_chain Bio::PDB::ChainFinder
#find_flat_dir Bio::Shell::Ghost
#find_hetatm Bio::PDB::HetatmFinder
#find_heterogen Bio::PDB::HeterogenFinder
#find_model Bio::PDB::ModelFinder
#find_residue Bio::PDB::ResidueFinder
#finder Bio::PDB::Utils
#first Bio::Locations
#first Bio::RestrictionEnzyme::DenseIntArray
#first Bio::Features
#first Bio::RestrictionEnzyme::DenseIntArray::MutableRange
#first Bio::RestrictionEnzyme::SortedNumArray
#first Bio::Genscan::Report::Exon
#flag Bio::FlatFileIndex::BDB_1::BDBMappingFile
flag_append Bio::FlatFileIndex::BDBdefault
flag_read Bio::FlatFileIndex::BDBdefault
flag_write Bio::FlatFileIndex::BDBdefault
#flatseq Bio::HMMER::Report::Hsp
#floyd_warshall Bio::Pathway
#fold String
#footer Bio::PAML::Codeml::Report
#for_display Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
#for_display Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
for_io Bio::PhyloXML::Parser
for_io Bio::FlatFile::BufferedInputStream
foreach Bio::FlatFile
#format Bio::Fastq
#format Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#format Bio::Blast
#format Bio::Reference
#format Bio::Fasta
#format Bio::FlatFileIndex::DataBank
#format= Bio::Fastq
#format= Bio::FlatFileIndex::DataBank
#format_raw Bio::Iprscan::Report
#formats Bio::Fetch
formatstring2class Bio::FlatFileIndex
#formul Bio::PDB::ChemicalComponent
#formula Bio::KEGG::DRUG
#formula Bio::KEGG::COMPOUND
#forward_complement Bio::Sequence::NA
#forward_complement! Bio::Sequence::NA
#found_again? Bio::Blast::Default::Report::Hit
#fp Bio::PTS1::Report
#fragments Bio::RestrictionEnzyme::Range::SequenceRange
#frame Bio::GFF::Record
#frame Bio::Genscan::Report::Exon
#from Bio::Location
#from Bio::Sim4::Report::Segment
#from Bio::Relation
#from Bio::Spidey::Report::Segment
#from Bio::PhyloXML::ProteinDomain
#ft Bio::EMBL
#ft Bio::TRANSFAC::FACTOR
#ft Bio::SPTR
#function Bio::PTS1
#gained Bio::PhyloXML::BinaryCharacters
#gained_count Bio::PhyloXML::BinaryCharacters
#gap_bases Bio::Blat::Report::SeqDesc
#gap_char Bio::Alignment::PropertyMethods
#gap_count Bio::Blat::Report::SeqDesc
#gap_extend Bio::Blast::Default::Report
#gap_extend Bio::Blast::Default::Report::F0dbstat
#gap_extend Bio::Blast::Report
#gap_length_weight Bio::GCG::Msf
#gap_open Bio::Blast::Default::Report
#gap_open Bio::Blast::Report
#gap_open Bio::Blast::Default::Report::F0dbstat
#gap_regexp Bio::Alignment::PropertyMethods
#gap_weight Bio::GCG::Msf
#gapped_entropy Bio::Blast::Default::Report::Iteration
#gapped_entropy Bio::Blast::Default::Report
#gapped_kappa Bio::Blast::Default::Report
#gapped_kappa Bio::Blast::Default::Report::Iteration
#gapped_lambda Bio::Blast::Default::Report
#gapped_lambda Bio::Blast::Default::Report::Iteration
gapped_pos Bio::Alignment::GAP
#gaps Bio::Blast::Report::Hsp
#gaps Bio::Blast::Default::Report::HSP
#gaps Bio::Spidey::Report::SegmentPair
#gbposition Bio::KEGG::GENES
#gc_content Bio::Sequence::NA
#gc_percent Bio::SiRNA::Pair
#gc_percent Bio::Sequence::NA
#gc_skew Bio::Sequence::NA
#gccontent Bio::Genscan::Report
#gene Bio::KEGG::GENES
#gene_name Bio::SPTR
#gene_name Bio::FANTOM::MaXML::Annotations
#gene_names Bio::SPTR
#gene_number Bio::Genscan::Report::Exon
#general Bio::Reference
generate Bio::Phylip::DistanceMatrix
#generate_colored_text Bio::Shell::ColoredCodonTable
#generate_mono_text Bio::Shell::ColoredCodonTable
generate_xml Bio::PhyloXML::Writer
#genes Bio::KEGG::GENES
#genes_as_hash Bio::KEGG::ORTHOLOGY
#genes_as_hash Bio::KEGG::PATHWAY
#genes_as_hash Bio::KEGG::Common::GenesAsHash
#genes_as_hash Bio::KEGG::ENZYME
#genes_as_strings Bio::KEGG::ENZYME
#genes_as_strings Bio::KEGG::ORTHOLOGY
#genes_as_strings Bio::KEGG::PATHWAY
#genome_biol Bio::Reference
#genome_res Bio::Reference
genomenet Bio::Blast::Remote
#genomic Bio::Spidey::Report::Hit
#genomic Bio::Spidey::Report::SegmentPair
#genscan_version Bio::Genscan::Report
#geodetic_datum Bio::PhyloXML::Point
#geometricCentre Bio::PDB::Utils
#get Bio::FastaDefline
#get Bio::FANTOM::MaXML::Sequences
#get Bio::Blast::NCBIOptions
#get Bio::DDBJ::REST::DDBJ
#get Bio::FlatFileIndex::FileID
#get Bio::DB
#getAllFeatures Bio::DDBJ::REST::DDBJ
#getAsyncResult Bio::DDBJ::REST::RequestManager
#getAsyncResult Bio::DDBJ::XML::RequestManager::REST
#getFFEntry Bio::DDBJ::REST::DDBJ
#getRelatedFeatures Bio::DDBJ::REST::DDBJ
#getRelatedFeaturesSeq Bio::DDBJ::REST::DDBJ
#getSupportDatabaseList Bio::DDBJ::REST::Blast
#get_aaseqs Bio::KEGG::API
#get_all_best_best_neighbors_by_gene Bio::KEGG::API
#get_all_best_neighbors_by_gene Bio::KEGG::API
#get_all_by_qualifier Bio::FANTOM::MaXML::Annotations
#get_all_by_type Bio::FastaDefline
#get_all_genes_by_motifs Bio::KEGG::API
#get_all_genes_by_organism Bio::KEGG::API
#get_all_linkdb_by_entry Bio::KEGG::API
#get_all_oc_members_by_gene Bio::KEGG::API
#get_all_paralogs_by_gene Bio::KEGG::API
#get_all_pc_members_by_gene Bio::KEGG::API
#get_all_property Bio::Alignment::PropertyMethods
#get_all_reverse_best_neighbors_by_gene Bio::KEGG::API
#get_attribute Bio::GFF::GFF2::Record
#get_attributes Bio::GFF::GFF2::Record
#get_blocks Bio::Nexus
#get_blocks_by_name Bio::Nexus
#get_by_id Bio::Blast::Fastacmd
get_by_id Bio::FANTOM
#get_by_id Bio::Fetch
#get_by_id Bio::FlatFileIndex
#get_by_qualifier Bio::FANTOM::MaXML::Annotations
#get_by_type Bio::FastaDefline
#get_characters_blocks Bio::Nexus
#get_characters_string Bio::Nexus::CharactersBlock
#get_characters_strings_by_name Bio::Nexus::CharactersBlock
#get_data_blocks Bio::Nexus
#get_database Bio::Registry
#get_datatype Bio::Nexus::CharactersBlock
#get_definitions Bio::KEGG::API
#get_distances_blocks Bio::Nexus
#get_dna Bio::DAS
#get_dsn Bio::DAS
#get_edge Bio::Tree
#get_edge_distance Bio::Tree
#get_edge_distance_string Bio::Tree
#get_edge_merged Bio::Tree
#get_entries Bio::KEGG::API
#get_entry Bio::FlatFile::Splitter::Default
#get_entry Bio::FlatFile::Splitter::LineOriented
#get_entry Bio::Blast::Report::BlastXmlSplitter
#get_entry Bio::Fasta::Report::FastaFormat10Splitter
#get_entry Bio::FlatFile::Splitter::Template
#get_entry Bio::Blast::RPSBlast::RPSBlastSplitter
#get_entry_points Bio::DAS
#get_features Bio::DAS
#get_flatfile_data Bio::FlatFileIndex::DataBank
#get_gap_character Bio::Nexus::CharactersBlock
#get_heterogen_by_id Bio::PDB::Chain
#get_match_character Bio::Nexus::CharactersBlock
#get_matrix Bio::Nexus::DistancesBlock
#get_matrix Bio::Nexus::CharactersBlock
#get_max_col Bio::Nexus::NexusMatrix
#get_max_row Bio::Nexus::NexusMatrix
#get_missing Bio::Nexus::CharactersBlock
#get_name Bio::Nexus::NexusMatrix
#get_name Bio::Nexus::GenericBlock
#get_naseqs Bio::KEGG::API
#get_node_bootstrap Bio::Tree
#get_node_bootstrap_string Bio::Tree
#get_node_by_name Bio::Tree
#get_node_name Bio::Tree
#get_number_of_characters Bio::Nexus::DistancesBlock
#get_number_of_characters Bio::Nexus::CharactersBlock
#get_number_of_taxa Bio::Nexus::DistancesBlock
#get_number_of_taxa Bio::Nexus::CharactersBlock
#get_number_of_taxa Bio::Nexus::TaxaBlock
#get_parsed_entry Bio::Blast::Report::BlastXmlSplitter
#get_parsed_entry Bio::FlatFile::Splitter::Template
#get_parsed_entry Bio::FlatFile::Splitter::LineOriented
#get_record Bio::FlatFileIndex::Flat_1::FlatMappingFile
get_record_class Bio::PDB::Record
get_record_class Bio::PDB::ChemicalComponent::Record
#get_residue_by_id Bio::PDB::Chain
get_residue_id_from_atom Bio::PDB::Residue
#get_row_name Bio::Nexus::CharactersBlock
#get_row_string Bio::Nexus::NexusMatrix
#get_row_strings_by_name Bio::Nexus::NexusMatrix
#get_seqfeature Bio::SQL::Sequence
#get_sequence Bio::ClustalW::Report
#get_sequence Bio::Nexus::CharactersBlock
#get_sequence Bio::DAS
#get_sequences_by_name Bio::Nexus::CharactersBlock
#get_taxa Bio::Nexus::DataBlock
#get_taxa Bio::Nexus::TaxaBlock
#get_taxa_blocks Bio::Nexus
#get_tokens Bio::Nexus::GenericBlock
#get_tree Bio::Nexus::TreesBlock
#get_tree_names Bio::Nexus::TreesBlock
#get_tree_strings Bio::Nexus::TreesBlock
#get_tree_strings_by_name Bio::Nexus::TreesBlock
#get_trees_blocks Bio::Nexus
#get_trees_by_name Bio::Nexus::TreesBlock
#get_triangle Bio::Nexus::DistancesBlock
#get_types Bio::DAS
#get_value Bio::Nexus::NexusMatrix
#getc Bio::FlatFile::BufferedInputStream
#getoptlong Bio::Shell::Setup
#gets Bio::FlatFile::BufferedInputStream
#gets Bio::FlatFile
#gff_version Bio::GFF::GFF3
#gff_version Bio::GFF::GFF2
#gi Bio::NCBIDB::Common
#gi Bio::FastaFormat
#gi Bio::FastaDefline
#glycans Bio::KEGG::COMPOUND
#gn Bio::SPTR
#go_ids Bio::GO::External2go
#go_terms Bio::Iprscan::Report::Match
#go_terms Bio::GO::External2go
#goid Bio::GO::GeneAssociation
#goid2term Bio::GO::Ontology
#gqual Bio::Scf
#grade Bio::SOSUI::Report::TMH
#graph Bio::Pathway
#graph Bio::PAML::Codeml::PositiveSites
#graph_omega Bio::PAML::Codeml::PositiveSites
#graph_seq Bio::PAML::Codeml::PositiveSites
#graph_to_s Bio::PAML::Codeml::PositiveSites
#graphics Bio::KEGG::KGML::Entry
#green Bio::PhyloXML::BranchColor
#groups Bio::DAS::FEATURE
#gss Bio::NCBI::REST::ESearch::Methods
#gsub_entities Bio::FANTOM::MaXML
#gt Bio::Location
#gtrace Bio::SangerChromatogram
guess Bio::Sequence
#guess Bio::Sequence
#guess Bio::FlatFile::AutoDetect::RuleRegexp
#guess Bio::FlatFile::AutoDetect::RuleRegexp2
#guess Bio::FlatFile::AutoDetect::RuleProc
#guess Bio::FlatFile::AutoDetect::RuleTemplate
#guess Bio::FlatFile::AutoDetect::RuleDebug
#has_gap? Bio::Alignment::SiteMethods
#has_key? Bio::Alignment::OriginalAlignment
#hash Bio::PDB
#hash Bio::PDB::ChemicalComponent
#hash Bio::Relation
#have_results BiorubyHelper
#hc_between_strands Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#hc_between_strands_as_original_class Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#hcuts Bio::RestrictionEnzyme::Range::HorizontalCutRange
#header Bio::PAML::Codeml::Report
#header Bio::Sequence::NA::MidiTrack
#header Bio::ClustalW::Report
#header Bio::Fastq
#header Bio::SOFT::Table
#header Bio::FlatFile::Splitter::Default
#header Bio::GO::External2go
#header_description Bio::SOFT::Table
#header_lines Bio::GO::Ontology
#header_object Bio::SOFT::Table::Row
#heading Bio::GCG::Msf
#heading Bio::GCG::Seq
#height Bio::KEGG::KGML::Entry
#height Bio::KEGG::KGML::Graphics
#height= Bio::KEGG::KGML::Entry
#helix Bio::PDB
#helix Bio::TMHMM::Report
#hetatm Bio::PDB::Residue
#hetatm Bio::PDB::Heterogen
#hetatms Bio::PDB::HetatmFinder
#heterogens Bio::PDB::Chain
#heterogens Bio::PDB::HeterogenFinder
#hetnam Bio::PDB::ChemicalComponent
#hetsyn Bio::PDB::ChemicalComponent
#hi Bio::SPTR
#higet_in_fasta Bio::HGC::HiGet
#higet_in_xml Bio::HGC::HiGet
#higher_priority_elements Bio::FlatFile::AutoDetect::RuleSpecial
#higher_priority_elements Bio::FlatFile::AutoDetect::RuleTemplate
#histogram Bio::HMMER::Report
#history BiorubyController
#history_file Bio::Shell::Core
hit2acc Bio::Hinv
hit_cnt Bio::Hinv
hit_definition Bio::Hinv
#hit_frame Bio::Blast::Default::Report::HSP
#hit_frame Bio::Blast::Report::Hsp
#hit_from Bio::Blast::Report::Hsp
#hit_from Bio::Spidey::Report::SegmentPair
#hit_from Bio::Blast::Default::Report::HSP
#hit_from Bio::Blat::Report::SegmentPair
#hit_from Bio::Sim4::Report::SegmentPair
#hit_id Bio::Blast::Report::Hit
hit_pubmedid Bio::Hinv
#hit_strand Bio::Blat::Report::SegmentPair
#hit_strand Bio::Blast::Default::Report::HSP
#hit_strand Bio::Spidey::Report::SegmentPair
#hit_to Bio::Spidey::Report::SegmentPair
#hit_to Bio::Blast::Default::Report::HSP
#hit_to Bio::Sim4::Report::SegmentPair
#hit_to Bio::Blast::Report::Hsp
#hit_to Bio::Blat::Report::SegmentPair
hit_xml Bio::Hinv
#hits Bio::Blast::Report
#hits Bio::Blast::Default::Report
#hits Bio::Spidey::Report
#hits Bio::Blat::Report
#hits Bio::Blast::Bl2seq::Report::Iteration
#hits Bio::Sim4::Report
#hits Bio::Blast::Report::Iteration
#hits Bio::HMMER::Report
#hits Bio::Fasta::Report
#hits Bio::Blast::Default::Report::Iteration
#hits_for_pattern Bio::Blast::Default::Report::Iteration
#hits_found_again Bio::Blast::Default::Report::Iteration
#hits_newly_found Bio::Blast::Default::Report::Iteration
hix2hit Bio::Hinv
hix_cnt Bio::Hinv
hix_represent Bio::Hinv
#hmm_f Bio::HMMER::Report::Hsp
#hmm_ft Bio::HMMER::Report::Hsp
#hmm_t Bio::HMMER::Report::Hsp
#hmmfile Bio::HMMER
#hmmseq Bio::HMMER::Report::Hsp
#ho Bio::TRANSFAC::FACTOR
#href Bio::FANTOM::MaXML::Annotation::DataSrc
#href Bio::DAS::LINK
#href Bio::DAS::GFF
#href Bio::DAS::ENTRY_POINT
#hseq Bio::Spidey::Report::SegmentPair
#hseq Bio::Blat::Report::SegmentPair
#hseq Bio::Sim4::Report::SegmentPair
#hseq Bio::Blast::Report::Hsp
#hseq Bio::Blast::Default::Report::HSP
#hsp Bio::Blast::Report::Hsp
#hsp_len Bio::Blast::Report
#hsps Bio::HMMER::Report::Hit
#hsps Bio::Blast::Report::Hit
#hsps Bio::HMMER::Report
#hsps Bio::Blast::Default::Report::Hit
http_post_form Bio::Command
human Bio::Ensembl
#iCode Bio::PDB::Residue
#icode Bio::Sequence::NA::MidiTrack
#id Bio::Sequence::DBLink
#id Bio::KEGG::KGML::Entry
#id Bio::PhyloXML::ProteinDomain
#id Bio::KEGG::KGML::Reaction
#id Bio::KEGG::KGML::SubstrateProduct
#id Bio::GFF::GFF3::Record
#id2id Bio::GO::Ontology
#id2term Bio::GO::Ontology
#id= Bio::GFF::GFF3::Record
#id_line Bio::SPTR
#id_line Bio::EMBL
#id_namespace Bio::Sequence
#id_ref Bio::PhyloXML::Property
#id_ref Bio::PhyloXML::Sequence
#id_ref_0 Bio::PhyloXML::CladeRelation
#id_ref_0 Bio::PhyloXML::SequenceRelation
#id_ref_1 Bio::PhyloXML::CladeRelation
#id_ref_1 Bio::PhyloXML::SequenceRelation
id_search Bio::Hinv
#id_source Bio::PhyloXML::Taxonomy
#id_source Bio::PhyloXML::Node
#id_source Bio::PhyloXML::Sequence
#id_strings Bio::FANTOM::MaXML::Sequence
#id_strings Bio::FANTOM::MaXML::Sequences
#id_strings Bio::FastaDefline
#identifier Bio::SQL::Sequence
#identifier= Bio::SQL::Sequence
#identifiers Bio::FastaFormat
#identity Bio::Fasta::Report::Hit
#identity Bio::Blast::Default::Report::HSP
#identity Bio::Blast::Report::Hsp
#identity Bio::Blast::Report::Hit
#identity Bio::Blast::Default::Report::Hit
#illegal_bases Bio::Sequence::NA
#image Bio::KEGG::KGML
#import_tsv_files Bio::FlatFileIndex::Flat_1::FlatMappingFile
imsut Bio::PSORT::PSORT2
imsut Bio::PSORT::PSORT1
#in Bio::TRANSFAC::FACTOR
#include? Bio::RestrictionEnzyme::Range::CutRanges
#include? Bio::RestrictionEnzyme::Range::VerticalCutRange
#include? Bio::RestrictionEnzyme::Range::HorizontalCutRange
#include? Bio::RestrictionEnzyme::DenseIntArray
#include? Bio::FlatFileIndex::Template::NameSpace
#include? Bio::RestrictionEnzyme::SortedNumArray
#include? Bio::Tree
#include? Bio::FlatFileIndex
#include_in_namespaces? Bio::FlatFileIndex
#include_in_primary? Bio::FlatFileIndex
#inclusion Bio::Blast::Report
#index Bio::AAindex1
#index Bio::Alignment::OriginalAlignment
#index Bio::Pathway
#index BiorubyController
#index_type Bio::FlatFileIndex::DataBank
#inhibitors Bio::KEGG::ENZYME
#init Bio::FlatFileIndex::Flat_1::FlatMappingFile
#init_fileids Bio::FlatFileIndex::DataBank
#init_with_sorted_tsv_file Bio::FlatFileIndex::Flat_1::FlatMappingFile
#initialize Bio::PROSITE
#initialize Bio::FlatFileIndex::BDBwrapper
#initialize Bio::PDB
#initialize Bio::Meme::Mast::Report
#initialize Bio::PAML::Codeml::Report
#initialize Bio::ClustalW::Report
#initialize Bio::KEGG::ENZYME
#initialize Bio::FlatFileIndex::Indexer::NameSpaces
#initialize Bio::MEDLINE
#initialize Bio::FlatFileIndex::NameSpaces
#initialize Bio::AAindex2
#initialize Bio::AAindex1
#initialize Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
#initialize Bio::AAindex
#initialize Bio::PSORT::PSORT2
#initialize Bio::PSORT::PSORT2::Remote
#initialize Bio::PSORT::PSORT1::Remote
#initialize Bio::PSORT::PSORT1
#initialize Bio::Fasta::Report::Hit
#initialize Bio::KEGG::PATHWAY
#initialize Bio::PSORT::CGIDriver
#initialize Bio::Blast::Default::Report::Hit
#initialize Bio::PhyloXML::Confidence
#initialize Bio::MAFFT
#initialize Bio::Fasta::Report::FastaFormat10Splitter
#initialize Bio::Blast::WU::Report::Hit
#initialize Bio::HMMER
#initialize Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#initialize Bio::FlatFileIndex::Flat_1::Record
#initialize Bio::TMHMM::TMH
#initialize Bio::FlatFile::AutoDetect::RuleSpecial
#initialize Bio::PAML::Common::Report
#initialize Bio::Blat::Report::SeqDesc
#initialize Bio::Fasta
#initialize Bio::Blast
#initialize Bio::PhyloXML::Node
#initialize Bio::Shell::Web::Results
#initialize Bio::Shell::Web
#initialize Bio::Blast::RPSBlast::RPSBlastSplitter
#initialize Bio::Shell::Irb
#initialize Bio::NCBIDB::Common
#initialize Bio::KEGG::MODULE
#initialize Bio::Alignment::MultiFastaFormat
#initialize Bio::Reference
#initialize Bio::Spidey::Report
#initialize Bio::ContingencyTable
#initialize Bio::PhyloXML::Sequence
#initialize Bio::TogoWS::REST
#initialize Bio::Blast::WU::Report::F0dbstat
#initialize Bio::REBASE
#initialize Bio::Newick
#initialize Bio::FANTOM::MaXML::Annotation::DataSrc
#initialize Bio::Blast::RPSBlast::Report
#initialize Bio::FANTOM::MaXML
#initialize Bio::Blast::Bl2seq::Report::Iteration
#initialize Bio::Sim4
#initialize Bio::PTS1::Report
#initialize Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
#initialize Bio::KEGG::COMPOUND
#initialize Bio::KEGG::REACTION
#initialize Bio::Alignment::FactoryTemplate::Simple
#initialize Bio::PhyloXML::BinaryCharacters
#initialize Bio::PSORT::PSORT2::Report
#initialize Bio::Sequence::NA::MidiTrack
#initialize Bio::PTS1
#initialize Bio::Blast::Report::Hit
#initialize Bio::Alignment::OriginalAlignment
#initialize Bio::Sequence::Format::Formatter::Fastq
#initialize Bio::RestrictionEnzyme::Range::SequenceRange
#initialize Bio::TMHMM::Report
#initialize Bio::Sim4::Report
#initialize Bio::PhyloXML::Writer
#initialize Bio::Scf
#initialize Bio::Blast::Report
#initialize Bio::Sequence
#initialize Bio::FlatFileIndex::Indexer::Parser::GenBankParser
#initialize Bio::RestrictionEnzyme::SortedNumArray
#initialize Bio::Locations
#initialize Bio::HGC::HiGet
#initialize Bio::Location
#initialize Bio::Fetch
#initialize Bio::Nexus::NexusMatrix
#initialize Bio::Nexus::TreesBlock
#initialize Bio::Nexus::DistancesBlock
#initialize Bio::Nexus::DataBlock
#initialize Bio::Nexus::CharactersBlock
#initialize Bio::GenBank::Locus
#initialize Bio::Nexus::TaxaBlock
#initialize Bio::RestrictionEnzyme::DoubleStranded
#initialize Bio::Nexus::GenericBlock
#initialize Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
#initialize Bio::Nexus
#initialize Bio::Blast::Default::Report::HSP
#initialize Bio::PAML::Codeml::PositiveSite
#initialize Bio::LITDB
#initialize Bio::Fastq
#initialize Bio::Fastq::FormatData
#initialize Bio::Blast::Default::Report::Iteration
#initialize Bio::FastaFormat
#initialize Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
#initialize Bio::Relation
#initialize Bio::MAFFT::Report
#initialize Bio::Spidey::Report::SeqDesc
#initialize Bio::Pathway
#initialize Bio::Hinv::IdSearch
#initialize Bio::Hinv::KeywordSearch
#initialize Bio::Spidey::Report::Hit
#initialize Bio::Hinv::HixRepresent
#initialize Bio::Hinv::HixCnt
#initialize Bio::Hinv::Hix2hit
#initialize Bio::Hinv::HitXML
#initialize Bio::Fasta::Report
#initialize Bio::Hinv::HitDefinition
#initialize Bio::Genscan::Report::Gene
#initialize Bio::Hinv::Hit2acc
#initialize Bio::Hinv::Acc2hit
#initialize Bio::Hinv::HitCnt
#initialize Bio::Feature::Qualifier
#initialize Bio::Hinv::HitPubmedId
#initialize Bio::Feature
#initialize Bio::TargetP::Report
#initialize Bio::SOFT::Table::Header
#initialize Bio::SOFT::Table::Row
#initialize Bio::SOFT::Table
#initialize Bio::SOFT
#initialize Bio::Sim4::Report::SegmentPair
#initialize Bio::NBRF
#initialize Bio::Blast::RPSBlast::Report::Iteration
#initialize Bio::FlatFile::AutoDetect
#initialize Bio::PAML::Codeml::ReportSingle
#initialize Bio::KEGG::ORTHOLOGY
#initialize Bio::Command::Tmpdir
#initialize Bio::Command::Tmpdir::Remover
#initialize Bio::References
#initialize Bio::FlatFile::AutoDetect::RuleRegexp
#initialize Bio::Blast::WU::Report::Iteration
#initialize Bio::DAS::GROUP
#initialize Bio::RestrictionEnzyme::DoubleStranded::CutLocations
#initialize Bio::PhyloXML::Polygon
#initialize Bio::Shell::ColoredCodonTable
#initialize Bio::FlatFile::Splitter::LineOriented
#initialize Bio::DAS::FEATURE
#initialize Bio::DAS::GFF
#initialize Bio::Features
#initialize Bio::SQL::Sequence
#initialize Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
#initialize Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#initialize Bio::FlatFile::AutoDetect::RuleDebug
#initialize Bio::FlatFile::AutoDetect::RuleTemplate
#initialize Bio::DAS::ENTRY_POINT
#initialize Bio::DAS::SEGMENT
#initialize Bio::PhyloXML::Other
#initialize Bio::DAS
#initialize Bio::GFF::GFF3::RecordBoundary
#initialize Bio::HMMER::Report::Hsp
#initialize Bio::GFF::GFF3::Record::Gap
#initialize Bio::GFF::GFF3::Record
#initialize Bio::FlatFileIndex
#initialize Bio::GFF::GFF3::Record::Target
#initialize Bio::GFF::GFF3::SequenceRegion
#initialize Bio::GFF::GFF3
#initialize Bio::GFF::GFF2::MetaData
#initialize Bio::FlatFileIndex::Indexer::NameSpace
#initialize Bio::GFF::GFF2
#initialize Bio::GFF::GFF2::Record
#initialize Bio::GFF::Record
#initialize Bio::GFF::GFF2::Record::Value
#initialize Bio::Genscan::Report::Exon
#initialize Bio::GFF
#initialize Bio::GO::External2go
#initialize Bio::PhyloXML::Parser
#initialize Bio::GO::GeneAssociation
#initialize Bio::FlatFile::AutoDetect::RuleProc
#initialize Bio::SOSUI::Report::TMH
#initialize Bio::GO::Ontology
#initialize Bio::RestrictionEnzyme::DenseIntArray
#initialize Bio::HMMER::Report
#initialize Bio::Blast::Default::Report
#initialize Bio::Tree
#initialize Bio::Blast::Report::BlastXmlSplitter
#initialize Bio::Tree::Node
#initialize Bio::Map::Marker
#initialize Bio::Tree::Edge
#initialize Bio::PAML::Codeml::Rates
#initialize Bio::Map::SimpleMap
#initialize Bio::Map::Mapping
#initialize Bio::SOSUI::Report
#initialize Bio::FlatFileIndex::BDB_1::BDBMappingFile
#initialize Bio::NCBIDB
#initialize Bio::EMBLDB
#initialize Bio::FastaDefline
#initialize Bio::KEGG::DRUG
#initialize Bio::Blat::Report::Hit
#initialize Bio::Abif
#initialize Bio::RestrictionEnzyme::SingleStrand
#initialize Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
#initialize Bio::FlatFile::BufferedInputStream
#initialize Bio::Blat::Report::SegmentPair
#initialize Bio::GCG::Seq
#initialize Bio::Phylip::PhylipFormat
#initialize Bio::GCG::Msf
#initialize Bio::PhyloXML::DomainArchitecture
#initialize Bio::Shell::Setup
#initialize Bio::Sim4::Report::SeqDesc
#initialize Bio::FlatFile::Splitter::Template
#initialize Bio::KEGG::GLYCAN
#initialize Bio::Sequence::NA
#initialize Bio::SOAPWSDL
#initialize Bio::Registry::DB
#initialize Bio::Sequence::AA
#initialize Bio::KEGG::EXPRESSION
#initialize Bio::Registry
#initialize Bio::NCBI::SOAP
#initialize Bio::Spidey::Report::SegmentPair
#initialize Bio::PhyloXML::Taxonomy
#initialize Bio::GenPept::Locus
#initialize Bio::Sequence::Format::Formatter::Qual
#initialize Bio::FlatFileIndex::FileID
#initialize Bio::FlatFileIndex::DataBank
#initialize Bio::Blast::Fastacmd
#initialize Bio::FlatFile
#initialize Bio::TRANSFAC::GENE
#initialize Bio::TRANSFAC::CLASS
#initialize Bio::TRANSFAC::CELL
#initialize Bio::Fasta::Report::Hit::Query
#initialize Bio::TRANSFAC::FACTOR
#initialize Bio::FlatFile::AutoDetect::RuleRegexp2
#initialize Bio::TRANSFAC::SITE
#initialize Bio::Sim4::Report::Hit
#initialize Bio::TRANSFAC::MATRIX
#initialize Bio::TRANSFAC
#initialize Bio::HMMER::Report::Hit
#initialize Bio::Blast::Report::Iteration
#initialize Bio::EMBOSS
#initialize Bio::Spidey::Report::Segment
#initialize Bio::Blast::NCBIOptions
#initialize Bio::Fasta::Report::Program
#initialize Bio::PAML::Codeml::PositiveSites
#initialize Bio::SiRNA::Pair
#initialize Bio::PAML::Codeml::Model
#initialize Bio::Blat::Report
#initialize Bio::PhyloXML::Tree
#initialize Bio::SiRNA
#initialize Bio::Shell::Demo
#initialize Bio::SiRNA::ShRNA
#initialize Bio::FlatFileIndex::Template::NameSpace
#initialize Bio::Phylip::DistanceMatrix
#initialize Bio::Sequence::Format::Formatter::Fasta
#initialize Bio::FlatFile::Splitter::Default
#initialize Bio::Meme::Motif
#initialize Bio::KEGG::GENOME
#initialize Bio::FlatFileIndex::Indexer::Parser::EMBLParser
#initialize Bio::Sequence::Format::Formatter::Fasta_numeric
#initialize Bio::Genscan::Report
#initialize Bio::FlatFileIndex::Flat_1::FlatMappingFile
#initialize Bio::KEGG::API
#initialize Bio::EBI::SOAP
#initialize Bio::Ensembl
#initialize Bio::DDBJ::XML
#initialize Bio::Blast::Report::Hsp
#initialize Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
#initialize Bio::PhyloXML::Distribution
#initialize Bio::KEGG::Keggtab::DB
#initialize Bio::RestrictionEnzyme::Range::VerticalCutRange
#initialize Bio::PhyloXML::Annotation
#initialize Bio::Sequence::Format::FormatterBase
#initialize Bio::KEGG::Keggtab
#initialize Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
#initialize Bio::Sequence::DBLink
#initialize Bio::PDB::Residue
#initialize Bio::FlatFileIndex::FileIDs
#initialize Bio::KEGG::GENES
#initialize Bio::KEGG::BRITE
#initialize Bio::PSORT::PSORT1::Report
#initialize Bio::ClustalW
#initialize Bio::Shell::Script
#initialize Bio::PAML::Common
#initialize Bio::Blast::Default::Report::F0dbstat
#initialize Bio::Taxonomy
#initialize Bio::PDB::Chain
#initialize Bio::Lasergene
#initialize Bio::PDB::Model
#initialize Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
#initialize Bio::Iprscan::Report::Match
#initialize Bio::KEGG::KGML::SubstrateProduct
#initialize Bio::RestrictionEnzyme::Range::HorizontalCutRange
#initialize Bio::Sim4::Report::Segment
#initialize Bio::PDB::ChemicalComponent
#initialize Bio::Iprscan::Report
#initialize Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
#initialize Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
#initialize Bio::CodonTable
#initialize Bio::KEGG::KGML
#initialize Bio::FlatFileIndex::Indexer::Parser::SPTRParser
#initialize Bio::EMBLDB::Common
#initialize Bio::Meme::Mast
#initialize_copy Bio::RestrictionEnzyme::DenseIntArray
#initialize_copy Bio::RestrictionEnzyme::SortedNumArray
#initialize_from_string Bio::PDB::Record
input Bio::Sequence
#insert_node Bio::Tree
#inspect Bio::PDB
#inspect Bio::FlatFile::AutoDetect
#inspect Bio::PDB::Record
#inspect Bio::PDB::Residue
#inspect Bio::FlatFile::AutoDetect::RulesArray
#inspect Bio::Tree::Node
#inspect Bio::Tree::Edge
#inspect Bio::PDB::Model
#inspect Bio::PDB::Chain
#install_savedir Bio::Shell::Setup
#interleaved? Bio::Phylip::PhylipFormat
#internal_http Bio::TogoWS::REST
internal_sort_proc Bio::FlatFileIndex::Flat_1::FlatMappingFile
#introns Bio::Spidey::Report::Hit
#introns Bio::Sim4::Report::Hit
#io Bio::FlatFile
#io Bio::EMBOSS
#ip Bio::MEDLINE
#ipr_id Bio::Iprscan::Report::Match
#ipr_odescription Bio::Iprscan::Report::Match
#is_aligned Bio::PhyloXML::Sequence
#is_aligned? Bio::PhyloXML::Sequence
#is_empty? Bio::Nexus::NexusMatrix
#is_gap? Bio::Alignment::PropertyMethods
#is_prior_to Bio::FlatFile::AutoDetect::RuleTemplate
#isochore Bio::Genscan::Report
#isolate Bio::Alignment::OriginalAlignment
#issue Bio::Reference
#iterations Bio::Blast::Default::Report
#iterations Bio::Blast::Report
#iubmb_reactions Bio::KEGG::ENZYME
#journal Bio::AAindex
#journal Bio::Reference
#journal Bio::LITDB
#journal Bio::NCBI::REST::EFetch::Methods
#journal Bio::NCBI::REST::ESearch::Methods
#jrnl Bio::PDB
#k Bio::PSORT::PSORT2::Report
#kappa Bio::Blast::Default::Report::Iteration
#kappa Bio::Blast::Default::Report
#kappa Bio::PAML::Codeml::Model
#kappa Bio::Blast::Report
#kcf Bio::KEGG::GLYCAN
#kcf Bio::KEGG::DRUG
#kcf Bio::KEGG::COMPOUND
#kegg_reactions Bio::KEGG::ENZYME
keggapi_definition2tab Bio::Shell::Private
#keggclass Bio::KEGG::PATHWAY
#keggclass Bio::KEGG::ORTHOLOGY
#keggclass Bio::KEGG::GLYCAN
#keggclass Bio::KEGG::MODULE
#keggclass Bio::KEGG::GENES
#keggclasses Bio::KEGG::ORTHOLOGY
#keggclasses Bio::KEGG::GENES
#key Bio::FlatFileIndex::Flat_1::Record
#keys Bio::Alignment::OriginalAlignment
#keys Bio::FlatFileIndex::BDBwrapper
#keys Bio::FlatFileIndex::FileIDs
#keyword Bio::LITDB
keyword_search Bio::Hinv
#keywords Bio::PDB
#keywords Bio::NCBIDB::Common
#keywords Bio::Sequence
#ko_pathway Bio::KEGG::PATHWAY
#korg2taxo Bio::KEGG::Keggtab
#kruskal Bio::Pathway
#ktup Bio::Fasta
#kw Bio::EMBLDB::Common
#label Bio::KEGG::KGML::Entry
#label Bio::Pathway
#label Bio::DAS::GROUP
#label Bio::DAS::FEATURE
#label Bio::DAS::TYPE
#label Bio::DAS::SEGMENT
#label= Bio::KEGG::KGML::Entry
#lambda Bio::Blast::Default::Report::Iteration
#lambda Bio::Blast::Default::Report
#lambda Bio::Blast::Report
#lap_at Bio::Blast::Report::Hit
#lap_at Bio::Fasta::Report::Hit
#lap_at Bio::Blast::Default::Report::Hit
#lap_over Bio::Fasta::Report
larger_than_zero Bio::Nexus::Util
#last Bio::RestrictionEnzyme::DenseIntArray::MutableRange
#last Bio::RestrictionEnzyme::DenseIntArray
#last Bio::Features
#last Bio::RestrictionEnzyme::SortedNumArray
#last Bio::Locations
#last Bio::Genscan::Report::Exon
#lat Bio::PhyloXML::Point
#leaves Bio::Tree
#left Bio::RestrictionEnzyme::Range::SequenceRange
#left_padding Bio::RestrictionEnzyme::StringFormatting
#len Bio::Blast::Default::Report::Hit
#len Bio::Spidey::Report::SeqDesc
#len Bio::Sim4::Report::SeqDesc
#len Bio::Blast::Report::Hit
#length Bio::SQL::Sequence
#length Bio::FastaNumericFormat
#length Bio::GenPept
#length Bio::GenBank
#length Bio::GCG::Seq
#length Bio::GCG::Msf
#length Bio::Fasta::Report::Hit::Query
#length Bio::Genscan::Report
#length Bio::PhyloXML::DomainArchitecture
#length Bio::GenBank::Locus
#length Bio::Locations
#length Bio::FastaFormat
#length Bio::Meme::Motif
#length Bio::NBRF
#length Bio::GenPept::Locus
#length Bio::DAS::DNA
#length Bio::GFF::GFF3::Record::Gap::Code
#length Bio::Iprscan::Report::Match
#length Bio::Map::SimpleMap
#length= Bio::SQL::Sequence
#library_id Bio::FANTOM::MaXML::Sequence
#lineage Bio::KEGG::GENOME
#link Bio::KEGG::KGML::Entry
#link Bio::KEGG::KGML
#links Bio::DAS::GROUP
#links Bio::DAS::FEATURE
#list Bio::Fasta::Report
#list_classes BiorubyController
list_databases Bio::SQL
list_entries Bio::SQL
#list_falsenegative Bio::PROSITE
#list_falsepositive Bio::PROSITE
#list_ids Bio::FastaDefline
#list_methods BiorubyController
#list_methods Bio::SOAPWSDL
#list_modules BiorubyController
#list_output_formats Bio::Sequence::Format
#list_potentialhit Bio::PROSITE
#list_sequences Bio::DAS
#list_truepositive Bio::PROSITE
#list_unknown Bio::PROSITE
#list_xref Bio::PROSITE
#lnL Bio::PAML::Codeml::Model
#load_config Bio::Shell::Ghost
#load_config_file Bio::Shell::Ghost
#load_history Bio::Shell::Ghost
#load_history_file Bio::Shell::Ghost
#load_object Bio::Shell::Ghost
#load_object_file Bio::Shell::Ghost
#load_parameters Bio::PAML::Common
#load_plugin Bio::Shell::Ghost
#load_plugin_dir Bio::Shell::Ghost
#load_session Bio::Shell::Ghost
load_yaml Bio::REBASE
#loc Bio::TargetP::Report
local Bio::Fasta
local Bio::Blast
#local_variables BiorubyHelper
#location Bio::PhyloXML::Sequence
#location Bio::Map::Mapping
#locations Bio::KEGG::GENES
#locations Bio::Locations
#locations Bio::Feature
#locus Bio::GenBank
#locus Bio::FastaDefline
#locus Bio::GenPept
#locus Bio::NCBIDB::Common
#locus Bio::FastaFormat
#log Bio::ClustalW
#log Bio::SOAPWSDL
#log Bio::MAFFT
#log Bio::Fasta::Report
#log Bio::Sim4
#log_likelihood Bio::Tree::Edge
#logy_minus_logx Bio::KEGG::EXPRESSION
#long Bio::PhyloXML::Point
longer_than_zero Bio::Nexus::Util
#losses Bio::PhyloXML::Events
#lost Bio::PhyloXML::BinaryCharacters
#lost_count Bio::PhyloXML::BinaryCharacters
#lower_priority_elements Bio::FlatFile::AutoDetect::RuleTemplate
#lower_priority_elements Bio::FlatFile::AutoDetect::RuleSpecial
#lowest_common_ancestor Bio::Tree
#lstrip Bio::Alignment::OriginalAlignment
#lt Bio::Location
#ma Bio::TRANSFAC::MATRIX
#ma Bio::PROSITE
#ma2re Bio::PROSITE
make_cgi_params Bio::Command
make_cgi_params_key_value Bio::Command
make_command_line Bio::Command
#make_command_line_options Bio::Blast::NCBIOptions
make_command_line_unix Bio::Command
make_command_line_windows Bio::Command
make_default Bio::FlatFile::AutoDetect
makeindex Bio::FlatFileIndex
makeindexBDB Bio::FlatFileIndex::Indexer
makeindexFlat Bio::FlatFileIndex::Indexer
#manifest BiorubyGenerator
#map Bio::Map::Mapping
#mapmaster Bio::DAS::DSN
#mapped_to? Bio::Map::ActsLikeMarker
#mapping Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
#mapping Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
#mapping Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
#mapping Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
#mapping Bio::FlatFileIndex::Template::NameSpace
#mappings_as_map Bio::Map::SimpleMap
#mappings_as_marker Bio::Map::Marker
#mappings_on Bio::Map::ActsLikeMarker
#marker Bio::Map::Mapping
#mask Bio::Fastq
#mask_with_enumerator Bio::Sequence::SequenceMasker
#mask_with_error_probability Bio::Sequence::SequenceMasker
#mask_with_quality_score Bio::Sequence::SequenceMasker
#mass Bio::KEGG::GLYCAN
#mass Bio::KEGG::COMPOUND
#mass Bio::KEGG::DRUG
#match Bio::Blat::Report::Hit
#match_end Bio::Iprscan::Report::Match
#match_line Bio::Alignment::EnumerableExtension
#match_line Bio::ClustalW::Report
#match_line_amino Bio::Alignment::EnumerableExtension
#match_line_amino Bio::Alignment::SiteMethods
#match_line_nuc Bio::Alignment::EnumerableExtension
#match_line_nuc Bio::Alignment::SiteMethods
#match_start Bio::Iprscan::Report::Match
#matches Bio::Iprscan::Report
#matrix Bio::Phylip::DistanceMatrix
#matrix Bio::Genscan::Report
#matrix Bio::AAindex2
#matrix Bio::Fasta
#matrix Bio::Blast::Report
#matrix Bio::Blast
#matrix Bio::Blast::Default::Report
#matrix Bio::Blast::Default::Report::F0dbstat
#max Bio::RestrictionEnzyme::Range::CutRanges
max Bio::ColorScheme::Score
#max Bio::RestrictionEnzyme::Range::VerticalCutRange
#max Bio::RestrictionEnzyme::Range::HorizontalCutRange
#max Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
#max_gc_percent Bio::SiRNA
#max_intensity Bio::KEGG::EXPRESSION
#max_repeat Bio::PROSITE
#max_results Bio::KEGG::API
#max_vertical Bio::RestrictionEnzyme::Range::CutRanges
#maxids Bio::Fetch
#maximum Bio::PhyloXML::Date
#medline Bio::Reference
#memo Object
#merge Bio::Alignment::OriginalAlignment
#merge! Bio::Alignment::OriginalAlignment
#mesh Bio::Reference
#message Bio::Blast::Report::Iteration
#message Bio::Blast::Default::Report::Iteration
#message Bio::Blast::Report
#message Bio::Blast::Default::Report
#metadata Bio::GFF::GFF3
#metadata Bio::GFF::GFF2
#method Bio::DAS::FEATURE
#method Bio::DAS::TYPE
#method_id Bio::DAS::FEATURE
#method_missing Bio::Iprscan::Report::Match
#method_missing Bio::FastaDefline
#method_missing Bio::Registry::DB
#method_missing Bio::NCBI::SOAP
#method_missing Bio::NCBI::REST::ESearch::Methods
#method_missing Bio::KEGG::API
#method_missing Bio::REBASE
#method_missing Bio::REBASE::DynamicMethod_Hash
#method_missing Bio::Sequence
#method_missing Bio::Blast::Default::Report::AlwaysNil
method_missing Bio
#method_missing Bio::PhyloXML::Parser::ClosedPhyloXMLParser
#method_name Bio::Iprscan::Report::Match
#mh Bio::MEDLINE
#midline Bio::Blast::Report::Hsp
#midline Bio::Spidey::Report::SegmentPair
#midline Bio::HMMER::Report::Hsp
#midline Bio::Blast::Default::Report::Hit
#midline Bio::Sim4::Report::SegmentPair
#midline Bio::Blast::Report::Hit
#midline Bio::Blast::Default::Report::HSP
#milli_bad Bio::Blat::Report::Hit
#min Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
#min Bio::RestrictionEnzyme::Range::CutRanges
#min Bio::RestrictionEnzyme::Range::HorizontalCutRange
min Bio::ColorScheme::Score
#min Bio::RestrictionEnzyme::Range::VerticalCutRange
#min_gc_percent Bio::SiRNA
#min_vertical Bio::RestrictionEnzyme::Range::CutRanges
#minimum Bio::PhyloXML::Date
#mismatch Bio::Blat::Report::Hit
#mismatch_count Bio::Blast::Report::Hsp
#mismatches Bio::Spidey::Report::SegmentPair
#missing_char Bio::Alignment::PropertyMethods
#missing_mrna_ends Bio::Spidey::Report::Hit
#mito Bio::Shell::Demo
mktmpdir Bio::Command
#mm Bio::TRANSFAC::SITE
#mode Bio::FlatFileIndex::Flat_1::FlatMappingFile
#model Bio::PDB::Chain
#modelnum Bio::PAML::Codeml::Model
#models Bio::PDB
#models Bio::PAML::Codeml::Report
#modules_as_hash Bio::KEGG::Common::ModulesAsHash
#modules_as_hash Bio::KEGG::ORTHOLOGY
#modules_as_hash Bio::KEGG::PATHWAY
#modules_as_strings Bio::KEGG::ORTHOLOGY
#modules_as_strings Bio::KEGG::PATHWAY
#mol_seq Bio::PhyloXML::Sequence
#molecular_weight Bio::Sequence::NA
#molecular_weight Bio::Sequence::AA
#molecule Bio::SPTR
#molecule Bio::EMBL
#molecule_type Bio::Sequence
#moltype Bio::Fasta::Report::Hit::Query
#moltype Bio::Sequence
#moltype Bio::DAS::SEQUENCE
#motif Bio::KEGG::GENES
#motif Bio::Meme::Motif
#motifs Bio::KEGG::ENZYME
#motifs Bio::Meme::Mast::Report
#motifs_as_hash Bio::KEGG::GENES
#motifs_as_strings Bio::KEGG::GENES
mouse Bio::Ensembl
#mrna Bio::Spidey::Report::Hit
#mrna Bio::Spidey::Report
#mrna Bio::Spidey::Report::SegmentPair
#mx Bio::TRANSFAC::FACTOR
#n_number Bio::Blast::WU::Report::Hit
#n_s Bio::Blat::Report::Hit
#na Bio::TRANSFAC::MATRIX
#na Bio::Sequence
#nalen Bio::KEGG::GENOME
#nalen Bio::Fastq
#nalen Bio::FastaFormat
#nalen Bio::NBRF
#name Bio::KEGG::GLYCAN
#name Bio::KEGG::MODULE
#name Bio::KEGG::GENOME
#name Bio::KEGG::ENZYME
#name Bio::KEGG::GENES
#name Bio::Lasergene
#name Bio::KEGG::KGML::SubstrateProduct
#name Bio::KEGG::KGML::Reaction
#name Bio::KEGG::KGML::Relation
#name Bio::KEGG::KGML::Graphics
#name Bio::KEGG::KGML::Entry
#name Bio::KEGG::KGML
#name Bio::KEGG::DRUG
#name Bio::FlatFileIndex::Template::NameSpace
#name Bio::Abif::DirectoryEntry
#name Bio::TargetP::Report
#name Bio::KEGG::COMPOUND
#name Bio::PAML::Codeml::Model
#name Bio::PROSITE
#name Bio::KEGG::REACTION
#name Bio::PhyloXML::Tree
#name Bio::PhyloXML::Node
#name Bio::PhyloXML::Sequence
#name Bio::SQL::Sequence
#name Bio::FlatFile::AutoDetect::RuleTemplate
#name Bio::FlatFileIndex::Indexer::NameSpace
#name Bio::Fastq::FormatData
#name Bio::NucleicAcid::Data
#name Bio::AminoAcid::Data
#name Bio::DAS::TARGET
#name Bio::Tree::Node
#name Bio::Map::Marker
#name Bio::Map::SimpleMap
#name Bio::KEGG::ORTHOLOGY
#name Bio::Blat::Report::SeqDesc
#name Bio::KEGG::PATHWAY
#name Bio::KEGG::Keggtab
#name Bio::KEGG::Keggtab::DB
#name2one Bio::AminoAcid::Data
#name2three Bio::AminoAcid::Data
#name= Bio::SQL::Sequence
#name= Bio::FlatFile::AutoDetect::RuleSpecial
#name_by_abbrev Bio::KEGG::Keggtab
#names Bio::KEGG::ENZYME
#names Bio::KEGG::KGML::Entry
#names Bio::KEGG::DRUG
#names Bio::Sequence::NA
#names Bio::Sequence::AA
#names Bio::FlatFileIndex::NameSpaces
#names Bio::FlatFileIndex::Indexer::NameSpaces
#names Bio::KEGG::ORTHOLOGY
#names Bio::KEGG::COMPOUND
#names Bio::NucleicAcid::Data
#names Bio::AminoAcid::Data
#names_as_array Bio::KEGG::GENES
#namespaces Bio::FlatFileIndex
#nar Bio::Reference
#naseq Bio::Genscan::Report::Gene
#naseq Bio::GCG::Seq
naseq Bio::DBGET
#naseq Bio::Fastq
#naseq Bio::FastaFormat
#naseq Bio::NBRF
#nature Bio::Reference
#natype Bio::GenBank
#natype Bio::GenBank::Locus
#nb_sites Bio::PAML::Codeml::Report
#networks Bio::TargetP::Report
new Bio::FlatFileIndex::Indexer::Parser
new Bio::RestrictionEnzyme
new Bio::References
new Bio::DDBJ::XML::RequestManager
new Bio::PDB::DataType::Pdb_Real
new Bio::PDB::DataType::Pdb_StringRJ
new Bio::PDB::DataType::Pdb_Specification_list
new Bio::PDB::DataType::Pdb_SList
new Bio::PDB::DataType::Pdb_Integer
new Bio::PDB::DataType::Pdb_List
new Bio::PDB::DataType::Pdb_String
new Bio::PDB::DataType::Pdb_LString
new Bio::Alignment
new Bio::Blast::Remote::GenomeNet
new Bio::Features
new Bio::Blast::Remote::DDBJ
new2 Bio::MAFFT
new2 Bio::Alignment
new2 Bio::Alignment::OriginalAlignment
new_direct Bio::PDB::Record
new_from_sequences_na Bio::GFF::GFF3::Record::Gap
new_from_sequences_na_aa Bio::GFF::GFF3::Record::Gap
new_from_string Bio::FlatFileIndex::FileID
new_http Bio::Command
new_inherit Bio::PDB::Record
new_intron Bio::Spidey::Report::SegmentPair
new_orig Bio::DDBJ::XML::RequestManager
new_with_fungi_function Bio::PTS1
new_with_general_function Bio::PTS1
new_with_metazoa_function Bio::PTS1
#next_entry Bio::FlatFile
#next_tree Bio::PhyloXML::Parser
#nhx_parameters Bio::Tree::Node
#nhx_parameters Bio::Tree::Edge
#nid Bio::NCBIDB::Common
#node Bio::Relation
#node_id Bio::PhyloXML::Node
#nodes Bio::Pathway
#nodes Bio::Tree
#normalize Bio::Alignment::OriginalAlignment
#normalize! Bio::Blast::NCBIOptions
#normalize! Bio::Sequence::Common
#notes Bio::DAS::GROUP
#notes Bio::DAS::FEATURE
#notes Bio::Blast::WU::Report
#notice Bio::Blast::WU::Report
#nr Bio::PROSITE
#ntlen Bio::KEGG::GENES
#ntseq Bio::KEGG::GENES
#nucleotide Bio::NCBI::REST::EFetch::Methods
#nucleotide_databases Bio::Blast::Remote::Information
#num Bio::Blast::Default::Report::Iteration
#num Bio::HMMER::Report::Hit
#num Bio::Blast::Report::Hit
#num Bio::Blast::Report::Hsp
#num Bio::Blast::Report::Iteration
#num_codons Bio::PAML::Codeml::Report
#num_gene Bio::KEGG::GENOME
#num_hits Bio::Blast::Default::Report::F0dbstat
#num_hits Bio::Sim4::Report
#num_hits Bio::Blat::Report
#num_hits Bio::Blast::Default::Report
#num_hits Bio::Spidey::Report
#num_rna Bio::KEGG::GENOME
#num_sequences Bio::PAML::Codeml::Report
#number Bio::KEGG::KGML
#number Bio::Genscan::Report::Exon
#number Bio::Genscan::Report::Gene
#number Bio::Shell::Web::Results
#number_of_edges Bio::Tree
#number_of_elements Bio::Abif::DirectoryEntry
#number_of_exons Bio::Spidey::Report::Hit
#number_of_nodes Bio::Tree
#number_of_sequences Bio::Phylip::PhylipFormat
#number_of_sequences Bio::Alignment::HashExtension
#number_of_sequences Bio::Alignment::ArrayExtension
#number_of_sequences Bio::Alignment::EnumerableExtension
#number_of_splice_sites Bio::Spidey::Report::Hit
nwap Bio::MAFFT
nwns Bio::MAFFT
nwnsi Bio::MAFFT
#object_file Bio::Shell::Core
#obsolete? Bio::KEGG::ENZYME
#oc Bio::EMBLDB::Common
#oc Bio::TRANSFAC
#offset Bio::Fastq::FormatData
#og Bio::EMBLDB::Common
#oh Bio::SPTR
okazaki Bio::PSORT::PSORT2
okazaki Bio::PSORT::PSORT1
#old_matrix Bio::AAindex2
#omega Bio::PAML::Codeml::Model
#omega Bio::PAML::Codeml::PositiveSite
#omim Bio::NCBI::REST::EFetch::Methods
#one2name Bio::AminoAcid::Data
#one2three Bio::AminoAcid::Data
open Bio::FlatFile
open Bio::FlatFileIndex::DataBank
open Bio::Blast::Default::Report
open Bio::PhyloXML::Parser
open Bio::SangerChromatogram
open Bio::DB
open Bio::FlatFileIndex
#open Bio::FlatFileIndex::FileID
open Bio::FlatFileIndex::Flat_1::FlatMappingFile
#open Bio::FlatFileIndex::Flat_1::FlatMappingFile
#open Bio::FlatFileIndex::BDB_1::BDBMappingFile
open Bio::FlatFileIndex::BDB_1::BDBMappingFile
#open Bio::FlatFileIndex::BDBwrapper
open_file Bio::FlatFile
open_file Bio::FlatFile::BufferedInputStream
#open_flatfile Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#open_flatfile Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
#open_flatfile Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
#open_flatfile Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
#open_history Bio::Shell::Ghost
open_uri Bio::FlatFile
open_uri Bio::PhyloXML::Parser
open_uri Bio::FlatFile::BufferedInputStream
#opening_splash Bio::Shell::Ghost
#operator Bio::Locations
#option Bio::ClustalW
#option Bio::MAFFT
#option Bio::HMMER
#option Bio::Fasta
#option Bio::Blast
#option Bio::Sim4
#option= Bio::HMMER
#option= Bio::Blast
#option= Bio::Fasta
#options Bio::Meme::Mast
#options Bio::ClustalW
#options Bio::MAFFT
#options Bio::HMMER
#options Bio::Fasta
#options Bio::Blast
#options Bio::Blast::NCBIOptions
#options Bio::Newick
#options Bio::Sim4
#options Bio::Alignment::FactoryTemplate::Simple
#options Bio::Tree
#options Bio::PAML::Codeml
#options= Bio::PAML::Codeml
#order Bio::Alignment::OriginalAlignment
#order_number Bio::Tree::Node
#orf2ratio Bio::KEGG::EXPRESSION
#orf2rgb Bio::KEGG::EXPRESSION
#orf2val Bio::KEGG::EXPRESSION
#org Bio::KEGG::KGML
#organelle Bio::Sequence
#organism Bio::KEGG::GENES
#organism Bio::Ensembl
#organism Bio::NCBIDB::Common
#organism Bio::SQL::Sequence
#organism Bio::KEGG::PATHWAY
#organism= Bio::SQL::Sequence
#orientation Bio::RestrictionEnzyme::SingleStrand
#orientation Bio::DAS::FEATURE
#orientation Bio::DAS::SEGMENT
#orientation Bio::RestrictionEnzyme::SingleStrandComplement
#origin Bio::NCBIDB::Common
#origin Bio::PSORT::PSORT2::Remote
#origin Bio::PSORT::PSORT2
#origin Bio::PSORT::PSORT1::Remote
#origin Bio::PSORT::PSORT1
#origin Bio::PSORT::PSORT1::Report
#original_data Bio::PDB::Record
#original_databases Bio::KEGG::GENOME
#original_db Bio::KEGG::GENOME
#original_matrix Bio::Phylip::DistanceMatrix
#original_string Bio::Newick
#orthologs_as_array Bio::KEGG::MODULE
#orthologs_as_hash Bio::KEGG::GLYCAN
#orthologs_as_hash Bio::KEGG::ENZYME
#orthologs_as_hash Bio::KEGG::Common::OrthologsAsHash
#orthologs_as_hash Bio::KEGG::GENES
#orthologs_as_hash Bio::KEGG::REACTION
#orthologs_as_hash Bio::KEGG::PATHWAY
#orthologs_as_hash Bio::KEGG::MODULE
#orthologs_as_strings Bio::KEGG::GLYCAN
#orthologs_as_strings Bio::KEGG::ENZYME
#orthologs_as_strings Bio::KEGG::GENES
#orthologs_as_strings Bio::KEGG::REACTION
#orthologs_as_strings Bio::KEGG::PATHWAY
#orthologs_as_strings Bio::KEGG::MODULE
#os Bio::EMBLDB::Common
#os Bio::SPTR
#os Bio::EMBL
#os Bio::TRANSFAC
#other Bio::PhyloXML::Parser
#other Bio::PhyloXML::Tree
#other Bio::PhyloXML::Taxonomy
#other Bio::PhyloXML::Sequence
#other Bio::PhyloXML::Node
#other_seqids Bio::Sequence
#otu_names Bio::Phylip::DistanceMatrix
#otus Bio::Phylip::DistanceMatrix
out Bio::FlatFileIndex::DEBUG
out= Bio::FlatFileIndex::DEBUG
#out_degree Bio::Tree
#out_edges Bio::Tree
#output Bio::ClustalW
#output Object
#output Bio::Sequence::Format::Formatter::Fasta_numeric
#output Bio::Shell::ColoredCodonTable
#output Bio::Tree
#output Bio::Iprscan::Report
#output Bio::HMMER
#output Bio::MAFFT
#output Bio::Fasta
#output Bio::Blast
#output Bio::Shell::Web::Results
#output Bio::Sim4
#output Bio::PTS1::Report
#output Bio::PTS1
#output Bio::Alignment::FactoryTemplate::Simple
#output Bio::Alignment::Output
#output Bio::Sequence::Format::Formatter::Fasta_ncbi
#output Bio::Sequence::Format::Formatter::Raw
#output Bio::Sequence::Format::Formatter::Fastq
#output Bio::Sequence::Format::Formatter::Fasta
#output Bio::PAML::Common
#output Bio::Sequence::Format::FormatterBase
output Bio::Sequence::Format::FormatterBase
#output Bio::Sequence::Format
#output_clustal Bio::Alignment::Output
#output_dnd Bio::ClustalW
#output_dnd Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
#output_fasta Bio::Alignment::Output
#output_fasta Bio::Sequence::Format
#output_molphy Bio::Alignment::Output
#output_msf Bio::Alignment::Output
#output_newick Bio::Tree
#output_nhx Bio::Tree
#output_phylip Bio::Alignment::Output
#output_phylip_distance_matrix Bio::Tree
#output_phylipnon Bio::Alignment::Output
#overlap Bio::Fasta::Report::Hit
#overlap Bio::Blast::Default::Report::Hit
#overlap Bio::Blast::Report::Hit
#ox Bio::SPTR
#p Bio::RestrictionEnzyme::Range::SequenceRange::Bin
p2q Bio::Sequence::QualityScore::Solexa
p2q Bio::Sequence::QualityScore::Phred
#p_cut_left Bio::RestrictionEnzyme::Range::HorizontalCutRange
#p_cut_left Bio::RestrictionEnzyme::Range::VerticalCutRange
#p_cut_right Bio::RestrictionEnzyme::Range::HorizontalCutRange
#p_cut_right Bio::RestrictionEnzyme::Range::VerticalCutRange
#p_left Bio::RestrictionEnzyme::Fragment
#p_left Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#p_left Bio::RestrictionEnzyme::Range::SequenceRange
#p_right Bio::RestrictionEnzyme::Range::SequenceRange
#p_right Bio::RestrictionEnzyme::Fragment
#p_right Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#p_sum_n Bio::Blast::WU::Report::HSP
#p_value Bio::Genscan::Report::Exon
#pa Bio::PROSITE
#pa2re Bio::PROSITE
pa2re Bio::PROSITE
#pages Bio::MEDLINE
#pages Bio::Reference
#palindromic? Bio::RestrictionEnzyme::SingleStrand
#parameter Bio::HMMER::Report
#parameter_matrix Bio::Blast::WU::Report
#parameters Bio::Blast::Report
#parameters Bio::Blast::WU::Report
#parameters Bio::PAML::Common
#parent Bio::Tree
parse Bio::Spidey::Report::SeqDesc
parse Bio::Spidey::Report::SegmentPair
parse Bio::GFF::GFF3::Record::Gap
parse Bio::GFF::GFF3::Record::Target
#parse Bio::GFF::GFF3::Record
parse Bio::GFF::GFF3::Record
parse Bio::GFF::GFF3::SequenceRegion
#parse Bio::GFF::GFF3
#parse Bio::GFF::GFF2
parse Bio::GFF::GFF2::MetaData
#parse Bio::GFF::GFF2::Record
parse Bio::GFF::GFF2::Record
parse Bio::Sim4::Report::SegmentPair
parse Bio::Sim4::Report::SeqDesc
parse Bio::Blast::NCBIOptions
parse_embl_DR_line Bio::Sequence::DBLink
parse_goids Bio::GO::Ontology
#parse_primary Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#parse_primary Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
parse_ptxt Bio::Iprscan::Report
parse_ptxt_entry Bio::Iprscan::Report
parse_raw Bio::Iprscan::Report
parse_raw_entry Bio::Iprscan::Report
#parse_secondary Bio::FlatFileIndex::Indexer::Parser::TemplateParser
parse_txt Bio::Iprscan::Report
parse_txt_entry Bio::Iprscan::Report
parse_uniprot_DR_line Bio::Sequence::DBLink
#parsed_entry Bio::FlatFile::Splitter::Template
parser Bio::Genscan::Report::Exon
parser Bio::Fasta
parser Bio::GO::External2go
parser Bio::GO::GeneAssociation
parser Bio::PSORT::PSORT1::Report
parser Bio::PSORT::PSORT2::Report
#parsing Bio::PSORT::PSORT2::Remote
#parsing Bio::PSORT::PSORT1::Remote
#partial Bio::PROSITE
#path Bio::FlatFile
#path Bio::Command::Tmpdir
#path Bio::Tree
#path Bio::FlatFile::BufferedInputStream
#path Bio::KEGG::Keggtab
#path Bio::KEGG::Keggtab::DB
#pathway Bio::KEGG::GENES
#pathway Bio::KEGG::KGML::Entry
#pathways_as_hash Bio::KEGG::GLYCAN
#pathways_as_hash Bio::KEGG::ENZYME
#pathways_as_hash Bio::KEGG::Common::PathwaysAsHash
#pathways_as_hash Bio::KEGG::GENES
#pathways_as_hash Bio::KEGG::DRUG
#pathways_as_hash Bio::KEGG::REACTION
#pathways_as_hash Bio::KEGG::COMPOUND
#pathways_as_hash Bio::KEGG::PATHWAY
#pathways_as_hash Bio::KEGG::MODULE
#pathways_as_hash Bio::KEGG::ORTHOLOGY
#pathways_as_strings Bio::KEGG::GLYCAN
#pathways_as_strings Bio::KEGG::ENZYME
#pathways_as_strings Bio::KEGG::GENES
#pathways_as_strings Bio::KEGG::DRUG
#pathways_as_strings Bio::KEGG::MODULE
#pathways_as_strings Bio::KEGG::REACTION
#pathways_as_strings Bio::KEGG::COMPOUND
#pathways_as_strings Bio::KEGG::PATHWAY
#pathways_as_strings Bio::KEGG::ORTHOLOGY
#pathways_in_keggclass Bio::KEGG::ORTHOLOGY
#pattern Bio::RestrictionEnzyme::SingleStrand
#pattern Bio::Blast::Default::Report
#pattern Bio::Blast::Report
#pattern Bio::Blast::Default::Report::Iteration
#pattern_from Bio::Blast::Report::Hsp
#pattern_in_database Bio::Blast::Default::Report::Iteration
#pattern_positions Bio::Blast::Default::Report
#pattern_positions Bio::Blast::Default::Report::Iteration
#pattern_to Bio::Blast::Report::Hsp
#pdb Bio::Shell::Demo
#pdb_hetdic Bio::Shell::Demo
#pdb_xref Bio::PROSITE
#pdoc_xref Bio::PROSITE
#peak_indices Bio::SangerChromatogram
peking Bio::PSORT::PSORT2
peking Bio::PSORT::PSORT1
#percent_gaps Bio::Blast::Default::Report::HSP
#percent_identity Bio::Spidey::Report::Hit
#percent_identity Bio::Blast::Report::Hsp
#percent_identity Bio::Blast::Report::Hit
#percent_identity Bio::Blast::Default::Report::HSP
#percent_identity Bio::Sim4::Report::SegmentPair
#percent_identity Bio::Blat::Report::Hit
#percent_identity Bio::Spidey::Report::SegmentPair
#percent_positive Bio::Blast::Default::Report::HSP
#permission Bio::FlatFileIndex::BDB_1::BDBMappingFile
permission Bio::FlatFileIndex::BDBdefault
#pg Bio::MEDLINE
#phase Bio::DAS::FEATURE
#phase Bio::Genscan::Report::Exon
#phred_p2q Bio::Sequence::QualityScore::Phred
#phred_q2p Bio::Sequence::QualityScore::Phred
#phylogeny_id Bio::PhyloXML::Tree
#pii Bio::MEDLINE
#pikachu Bio::Sequence::NA
#plasmids Bio::KEGG::GENOME
#platform Bio::SOFT
#plugin_dir Bio::Shell::Core
#pmc Bio::NCBI::REST::EFetch::Methods
pmfetch Bio::PubMed
#pmfetch Bio::PubMed
#pmid Bio::MEDLINE
#points Bio::PhyloXML::Polygon
#points Bio::PhyloXML::Distribution
#polyA Bio::Genscan::Report::Gene
#polygons Bio::PhyloXML::Distribution
#pos Bio::FlatFile
#pos Bio::FlatFile::BufferedInputStream
#pos= Bio::FlatFile
#pos= Bio::FlatFile::BufferedInputStream
#position Bio::KEGG::GENES
#position Bio::PAML::Codeml::PositiveSite
#position Bio::Feature
#positions_on Bio::Map::ActsLikeMarker
#positive Bio::PROSITE
#positive Bio::Blast::Report::Hsp
#positive Bio::Blast::Default::Report::HSP
#positive_hits Bio::PROSITE
#positive_sequences Bio::PROSITE
post_form Bio::Command
#posted_date Bio::Blast::Default::Report
#posted_date Bio::Blast::Default::Report::F0dbstat
#posted_date Bio::Blast::Default::Report::Iteration
#pred Bio::PSORT::PSORT2::Report
#predicted_tmhs Bio::TMHMM::Report
#prediction Bio::PTS1::Report
#prediction Bio::TargetP::Report
#prediction Bio::SOSUI::Report
#predictions Bio::Genscan::Report
#prefetch_buffer Bio::FlatFile::BufferedInputStream
#prefetch_gets Bio::FlatFile::BufferedInputStream
#prefetch_readpartial Bio::FlatFile::BufferedInputStream
#present Bio::PhyloXML::BinaryCharacters
#present_count Bio::PhyloXML::BinaryCharacters
#primary Bio::RestrictionEnzyme::Fragment
#primary Bio::RestrictionEnzyme::Fragments
#primary Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
#primary Bio::RestrictionEnzyme::DoubleStranded
#primary Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands::Result
#primary Bio::FlatFileIndex::DataBank
#primary Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#primary Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
#primary Bio::RestrictionEnzyme::Range::SequenceRange::Fragments::DisplayFragment
#primary Bio::RestrictionEnzyme::DoubleStranded::CutLocations
#primary Bio::RestrictionEnzyme::Range::SequenceRange::Fragment::DisplayFragment
#primary= Bio::FlatFileIndex::DataBank
#primary_accession Bio::Sequence
#primary_accession Bio::SQL::Sequence
#primary_accession= Bio::SQL::Sequence
#primary_namespace Bio::FlatFileIndex
#primary_to_array_index Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
print Bio::FlatFileIndex::DEBUG
#prob Bio::PSORT::PSORT2::Report
#probability Bio::PAML::Codeml::PositiveSite
#proc Bio::FlatFileIndex::Indexer::NameSpace
#process_sequences_na Bio::GFF::GFF3::Record::Gap
#process_sequences_na_aa Bio::GFF::GFF3::Record::Gap
#products Bio::KEGG::ENZYME
#products Bio::KEGG::KGML::Reaction
#products Bio::KEGG::DRUG
#profile Bio::PTS1::Report
#program Bio::ClustalW
#program Bio::MAFFT
#program Bio::HMMER
#program Bio::Fasta
#program Bio::Blast
#program Bio::Fasta::Report::Program
#program Bio::Sim4
#program Bio::Alignment::FactoryTemplate::Simple
#program Bio::HMMER::Report
#program Bio::Blast::Report
#program Bio::Blast::Default::Report
#program Bio::Fasta::Report
#project_workdir BiorubyHelper
#promoter Bio::Genscan::Report::Gene
#properties Bio::PhyloXML::Annotation
#properties Bio::PhyloXML::Tree
#properties Bio::PhyloXML::Node
#protein Bio::NCBI::REST::EFetch::Methods
#protein? Bio::Blat::Report::Hit
#protein_databases Bio::Blast::Remote::Information
#protein_name Bio::SPTR
#provider Bio::PhyloXML::Id
#psl_version Bio::Blat::Report
#pt Bio::MEDLINE
#pubmed Bio::NCBI::REST::EFetch::Methods
#pubmed Bio::MEDLINE
#pubmed Bio::Reference
#pubmed_url Bio::Reference
#purge Bio::Alignment::OriginalAlignment
#push Bio::RestrictionEnzyme::SortedNumArray
#push Bio::RestrictionEnzyme::DenseIntArray
#push Bio::Sequence::NA::MidiTrack
#push_silent Bio::Sequence::NA::MidiTrack
#put_record Bio::FlatFileIndex::Flat_1::FlatMappingFile
#pvalue Bio::Blast::WU::Report::Hit
#pvalue Bio::Blast::WU::Report::HSP
#pvalue Bio::Meme::Motif
q2p Bio::Sequence::QualityScore::Phred
q2p Bio::Sequence::QualityScore::Solexa
#qseq Bio::Spidey::Report::SegmentPair
#qseq Bio::Blast::Report::Hsp
#qseq Bio::Sim4::Report::SegmentPair
#qseq Bio::Blast::Default::Report::HSP
#qseq Bio::Blat::Report::SegmentPair
#qualifier Bio::Feature::Qualifier
#qualifier Bio::GO::GeneAssociation
#qualifiers Bio::Feature
#qualities Bio::SangerChromatogram
#quality_score_type Bio::Sequence::QualityScore::Phred
#quality_score_type Bio::Sequence
#quality_score_type Bio::Sequence::QualityScore::Solexa
#quality_score_type Bio::Fastq
#quality_score_type Bio::Fastq::FormatData
#quality_scores Bio::Sequence
#quality_scores Bio::Fastq
#quality_string Bio::Fastq
#query Bio::PAML::Yn00
#query Bio::ClustalW
#query Bio::Registry
#query Bio::MAFFT
#query Bio::HMMER
#query Bio::Fasta
#query Bio::Blast
query Bio::PubMed
#query Bio::PubMed
#query Bio::Sim4
query Bio::FANTOM
#query Bio::Alignment::FactoryTemplate::Simple
query Bio::Fetch
#query Bio::FastaFormat
#query Bio::Hinv::IdSearch
#query Bio::Hinv::KeywordSearch
#query Bio::Hinv::Common
#query Bio::Fasta::Report::Hit
#query Bio::PAML::Common
#query Bio::PAML::Codeml
#query Bio::Blat::Report::Hit
#query_align Bio::ClustalW
#query_align Bio::MAFFT
#query_align Bio::Alignment::FactoryTemplate::Simple
#query_alignment Bio::ClustalW
#query_alignment Bio::MAFFT
#query_alignment Bio::Alignment::FactoryTemplate::Simple
#query_by_filename Bio::ClustalW
#query_by_filename Bio::MAFFT
#query_by_filename Bio::Alignment::FactoryTemplate::Simple
#query_by_string Bio::PAML::Yn00
#query_by_string Bio::PAML::Common
#query_by_string Bio::PAML::Codeml
query_command Bio::Command
query_command_fork Bio::Command
query_command_open3 Bio::Command
query_command_popen Bio::Command
#query_def Bio::Fasta::Report::Hit
#query_def Bio::Spidey::Report::Hit
#query_def Bio::Spidey::Report
#query_def Bio::Fasta::Report
#query_def Bio::Blast::RPSBlast::Report
#query_def Bio::Blast::RPSBlast::Report::Iteration
#query_def Bio::Blast::Report::Hit
#query_def Bio::Blast::Report
#query_def Bio::Blast::Report::Iteration
#query_def Bio::Sim4::Report::Hit
#query_def Bio::Blat::Report
#query_def Bio::Blat::Report::Hit
#query_def Bio::Sim4::Report
#query_def Bio::Blast::Default::Report
#query_end Bio::Blast::Report::Hit
#query_end Bio::Fasta::Report::Hit
#query_end Bio::Blast::Default::Report::Hit
#query_frame Bio::HMMER::Report::Hsp
#query_frame Bio::Blast::Report::Hsp
#query_frame Bio::Blast::Default::Report::HSP
#query_from Bio::HMMER::Report::Hsp
#query_from Bio::Blast::Report::Hsp
#query_from Bio::Sim4::Report::SegmentPair
#query_from Bio::Blat::Report::SegmentPair
#query_from Bio::Spidey::Report::SegmentPair
#query_from Bio::Blast::Default::Report::HSP
#query_id Bio::Fasta::Report::Hit
#query_id Bio::Iprscan::Report
#query_id Bio::Spidey::Report
#query_id Bio::Iprscan::Report::Match
#query_id Bio::Spidey::Report::Hit
#query_id Bio::Blast::Report::Hit
#query_id Bio::Blast::Report::Iteration
#query_id Bio::Blast::Report
#query_id Bio::Sim4::Report
#query_id Bio::Sim4::Report::Hit
#query_info Bio::HMMER::Report
#query_len Bio::Spidey::Report::Hit
#query_len Bio::Blast::RPSBlast::Report
#query_len Bio::Fasta::Report
#query_len Bio::Fasta::Report::Hit
#query_len Bio::Blast::RPSBlast::Report::Iteration
#query_len Bio::TMHMM::Report
#query_len Bio::Blast::Report::Hit
#query_len Bio::Blast::Report
#query_len Bio::Sim4::Report
#query_len Bio::Blast::Report::Iteration
#query_len Bio::Sim4::Report::Hit
#query_len Bio::Blat::Report::Hit
#query_len Bio::Blat::Report
#query_len Bio::Spidey::Report
#query_len Bio::Blast::Default::Report
#query_len Bio::TargetP::Report
#query_length Bio::Iprscan::Report
#query_name Bio::Genscan::Report
#query_pairwise Bio::Sim4
#query_record_number Bio::Blast::WU::Report
#query_seq Bio::Fasta::Report::Hit
#query_seq Bio::HMMER::Report::Hsp
#query_seq Bio::Blast::Report::Hit
#query_seq Bio::Blast::Default::Report::Hit
#query_sequences Bio::TargetP::Report
#query_start Bio::Fasta::Report::Hit
#query_start Bio::Blast::Default::Report::Hit
#query_start Bio::Blast::Report::Hit
#query_strand Bio::Blast::Default::Report::HSP
#query_strand Bio::Spidey::Report::SegmentPair
#query_strand Bio::Blat::Report::SegmentPair
#query_string Bio::ClustalW
#query_string Bio::MAFFT
#query_string Bio::Alignment::FactoryTemplate::Simple
#query_to Bio::Blast::Default::Report::HSP
#query_to Bio::HMMER::Report::Hsp
#query_to Bio::Blast::Report::Hsp
#query_to Bio::Sim4::Report::SegmentPair
#query_to Bio::Blat::Report::SegmentPair
#query_to Bio::Spidey::Report::SegmentPair
#query_type Bio::Fasta::Report::Hit
#ra Bio::TRANSFAC
rad2deg Bio::PDB::Utils
randomize Bio::Sequence::AA
randomize Bio::Sequence::NA
#randomize Bio::Sequence::Common
#range Bio::Genscan::Report::Exon
#range Bio::Locations
#range Bio::Location
#range Bio::RestrictionEnzyme::Range::VerticalCutRange
#range Bio::TMHMM::TMH
#range Bio::SOSUI::Report::TMH
#rank Bio::Taxonomy
#raw Bio::FlatFile
#raw Bio::ClustalW::Report
#raw Bio::PSORT::PSORT1::Report
#raw Bio::PSORT::PSORT2::Report
#rc Bio::TargetP::Report
#rcode Bio::Sequence::NA::MidiTrack
#rd Bio::Reference
#re Bio::TRANSFAC::SITE
#re Bio::PROSITE
#re_cut_symbol Bio::RestrictionEnzyme::CutSymbol
#re_cut_symbol_adjacent Bio::RestrictionEnzyme::CutSymbol
#reaction Bio::KEGG::ENZYME
#reaction Bio::KEGG::KGML::Entry
#reactions Bio::KEGG::GLYCAN
#reactions Bio::KEGG::KGML
#reactions Bio::KEGG::COMPOUND
#reactions_as_hash Bio::KEGG::PATHWAY
#reactions_as_hash Bio::KEGG::MODULE
#reactions_as_strings Bio::KEGG::PATHWAY
#reactions_as_strings Bio::KEGG::MODULE
read Bio::REBASE
read Bio::Sequence
read Bio::FlatFileIndex::DataBank
#read Bio::FlatFileIndex::FileID
read_uri Bio::Command
readfiles Bio::Alignment
readfiles Bio::Alignment::OriginalAlignment
#reasoning Bio::PSORT::PSORT1::Report
rebase Bio::RestrictionEnzyme
#recalc Bio::FlatFileIndex::FileID
#recalc_all Bio::FlatFileIndex::FileIDs
#record Bio::PDB
#record Bio::PDB::ChemicalComponent
#record_name Bio::PDB::Record
#record_size Bio::FlatFileIndex::Flat_1::FlatMappingFile
#records Bio::GFF
#records Bio::FlatFileIndex::Flat_1::FlatMappingFile
#records Bio::FlatFileIndex::BDB_1::BDBMappingFile
#red Bio::PhyloXML::BranchColor
#ref Bio::EMBLDB::Common
#ref Bio::SPTR
#ref Bio::PhyloXML::Annotation
#ref Bio::PhyloXML::Property
#reference Bio::MEDLINE
#reference Bio::LITDB
#reference Bio::DAS::TYPE
#reference Bio::Blast::Report
#reference Bio::Blast::Default::Report
#reference= Bio::SQL::Sequence
#reference_link BiorubyHelper
#references Bio::KEGG::GLYCAN
#references Bio::KEGG::GENOME
#references Bio::KEGG::Common::References
#references Bio::EMBLDB::Common
#references Bio::SPTR
#references Bio::Sequence
#references Bio::SQL::Sequence
#references Bio::Blast::Default::Report
#references Bio::PhyloXML::Node
#references Bio::NCBIDB::Common
#references Bio::KEGG::ORTHOLOGY
#references Bio::References
#references Bio::References::BackwardCompatibility
#references Bio::KEGG::PATHWAY
region Bio::DAS::SEGMENT
#regulated Bio::KEGG::EXPRESSION
#rehash Bio::PDB::Model
#rehash Bio::PDB::Chain
#rehash Bio::Alignment::OriginalAlignment
#rehash Bio::FlatFile::AutoDetect
#rehash_heterogens Bio::PDB::Chain
#rehash_residues Bio::PDB::Chain
#rel_pathways_as_hash Bio::KEGG::PATHWAY
#rel_pathways_as_strings Bio::KEGG::PATHWAY
#relation Bio::Relation
#relations Bio::KEGG::KGML
#relations Bio::Pathway
#relative Bio::Locations
#release Bio::PROSITE
#release_created Bio::EMBL
#release_created Bio::Sequence
#release_modified Bio::EMBL
#release_modified Bio::Sequence
#reload_script BiorubyController
#remark Bio::KEGG::GLYCAN
#remark Bio::KEGG::DRUG
#remark Bio::PDB
#remark Bio::KEGG::COMPOUND
remote Bio::PSORT::PSORT2
remote Bio::Fasta
remote Bio::Blast
#removeSolvent Bio::PDB::Model
#remove_all_gaps Bio::Alignment::OriginalAlignment
#remove_all_gaps! Bio::Alignment::EnumerableExtension
#remove_edge Bio::Tree
#remove_edge_if Bio::Tree
remove_entry_secure Bio::Command
#remove_gaps! Bio::Alignment::SiteMethods
#remove_incomplete_cuts Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#remove_node Bio::Tree
#remove_node_if Bio::Tree
#remove_nonsense_nodes Bio::Tree
#remove_seq Bio::Alignment::OriginalAlignment
#render_log BiorubyHelper
#rep_accession_no Bio::Hinv::HixRepresent
#rep_match Bio::Blat::Report::Hit
#reparse Bio::Newick
#replace Bio::Location
#replace_attributes Bio::GFF::GFF2::Record
#replace_slice Bio::Alignment::OriginalAlignment
#report Bio::ClustalW
#report Bio::SiRNA::ShRNA
#report Bio::SiRNA::Pair
#report Bio::PSORT::CGIDriver
#report Bio::MAFFT
#report Bio::Sim4
#report Bio::Alignment::FactoryTemplate::Simple
#report Bio::PAML::Common
reports Bio::Blast
reports Bio::TMHMM
reports Bio::HMMER
#reports Bio::Blast::Report
reports_xml Bio::Blast
#representative_annotations Bio::FANTOM::MaXML::Cluster
#representative_cloneid Bio::FANTOM::MaXML::Cluster
#representative_seqid Bio::FANTOM::MaXML::Cluster
#representative_sequence Bio::FANTOM::MaXML::Cluster
#rerootable Bio::PhyloXML::Tree
#resName Bio::PDB::Residue
#resSeq Bio::PDB::Residue
#reset Bio::ClustalW
#reset Bio::MAFFT
#reset Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
#reset Bio::Alignment::FactoryTemplate::Simple
#reset Bio::Blast::Remote::Information
reset_entrez_default_parameters Bio::NCBI
#residue Bio::PDB::Record::ATOM
#residue_id Bio::PDB::Residue
#residues Bio::PDB::ResidueFinder
#residues Bio::PDB::Chain
#restore Bio::Shell::Web::Results
#result Bio::EMBOSS
#result Bio::Shell::Web::Results
#result Bio::Hinv::KeywordSearch
#result Bio::Hinv::HixCnt
#result Bio::Hinv::HitPubmedId
#result Bio::Hinv::HitXML
#result Bio::Hinv::Hix2hit
#result Bio::Hinv::HixRepresent
#result Bio::Hinv::HitCnt
#result Bio::Hinv::HitDefinition
#result Bio::Hinv::Hit2acc
#result Bio::Hinv::Acc2hit
#result_info Bio::PSORT::PSORT1::Report
#results BiorubyController
retrieve Bio::TogoWS::REST
#retrieve Bio::TogoWS::REST
#reverse_complement Bio::Sequence::NA
#reverse_complement! Bio::Sequence::NA
#reverse_each Bio::RestrictionEnzyme::SortedNumArray
#reverse_each Bio::RestrictionEnzyme::DenseIntArray
#revtrans Bio::CodonTable
#rewind Bio::FlatFile
#rewind Bio::FlatFile::BufferedInputStream
#rewind Bio::FlatFile::Splitter::Template
#rewind Bio::FlatFile::Splitter::LineOriented
#rewind Bio::Blast::Report::BlastXmlSplitter
#rewind Bio::Blast::RPSBlast::RPSBlastSplitter
rexml Bio::Blast::Report
#reynolds Bio::SiRNA
#reynolds? Bio::SiRNA
#rfline Bio::HMMER::Report::Hsp
#right Bio::RestrictionEnzyme::Range::SequenceRange
#right_padding Bio::RestrictionEnzyme::StringFormatting
#rl Bio::TRANSFAC
#rn Bio::TRANSFAC
#rna Bio::Sequence::NA
#rna! Bio::Sequence::NA
#root Bio::Tree
#rooted Bio::PhyloXML::Tree
#row_sum Bio::ContingencyTable
#row_sum_all Bio::ContingencyTable
#rows Bio::AAindex2
#rows Bio::SOFT::Table
#rpairs Bio::KEGG::COMPOUND
#rpairs_as_hash Bio::KEGG::REACTION
#rpairs_as_strings Bio::KEGG::REACTION
#rpairs_as_tokens Bio::KEGG::REACTION
#rstrip Bio::Alignment::OriginalAlignment
#rt Bio::TRANSFAC
#ru Bio::PROSITE
#rule Bio::SiRNA::Pair
#run Bio::Meme::Mast
run Bio::EMBOSS
#run Bio::PAML::Common
#s1 Bio::TRANSFAC::SITE
safe_command_line_array Bio::Command
#sample_title Bio::Abif
#samples Bio::SOFT
#save Bio::SQL::Sequence
#save_config Bio::Shell::Ghost
#save_config_file Bio::Shell::Ghost
#save_history Bio::Shell::Ghost
#save_history_file Bio::Shell::Ghost
#save_image Bio::KEGG::API
#save_object Bio::Shell::Ghost
#save_object_file Bio::Shell::Ghost
#save_script Bio::Shell::Ghost
#save_script_file Bio::Shell::Ghost
#save_session Bio::Shell::Ghost
#save_yaml Bio::REBASE
#sc Bio::TRANSFAC::FACTOR
#sc_match Bio::Blast::Report
#sc_match Bio::Blast::Default::Report::F0dbstat
#sc_match Bio::Blast::Default::Report
#sc_mismatch Bio::Blast::Report
#sc_mismatch Bio::Blast::Default::Report::F0dbstat
#sc_mismatch Bio::Blast::Default::Report
#science Bio::Reference
#scientific_name Bio::Tree::Node
#scientific_name Bio::Taxonomy
#scl Bio::PSORT::PSORT2::Report
#score Bio::PTS1::Report
#score Bio::DAS::FEATURE
#score Bio::GFF::Record
#score Bio::Blast::Default::Report::Hit
#score Bio::Fasta::Report::Hit
#score Bio::Genscan::Report::Exon
#score Bio::HMMER::Report::Hsp
#score Bio::HMMER::Report::Hit
#score Bio::Blast::Report::Hsp
#score Bio::Blat::Report::Hit
#score Bio::Blast::WU::Report::Hit
#score Bio::Blast::Default::Report::HSP
#score_range Bio::Fastq::FormatData
scores Bio::ColorScheme::Score
#scores2str Bio::Fastq::FormatData
#script Bio::Shell::Ghost
#script Bio::Shell::Web::Results
#script_begin Bio::Shell::Ghost
#script_dir Bio::Shell::Core
#script_end Bio::Shell::Ghost
#script_file Bio::Shell::Core
#sd Bio::TRANSFAC::GENE
#sd Bio::TRANSFAC::CLASS
#search Bio::NCBI::REST::ESearch::Methods
search Bio::TogoWS::REST
#search Bio::TogoWS::REST
search Bio::PubMed
#search Bio::PubMed
#search Bio::FlatFileIndex::NameSpaces
#search Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
#search Bio::FlatFileIndex::Flat_1::FlatMappingFile
#search Bio::FlatFileIndex::Template::NameSpace
#search Bio::FlatFileIndex
#search Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
#search Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
#search Bio::FlatFileIndex::BDB_1::BDBMappingFile
#searchParallel Bio::DDBJ::REST::Blast
#searchParallelAsync Bio::DDBJ::REST::Blast
#searchParam Bio::DDBJ::REST::Blast
#searchParamAsync Bio::DDBJ::REST::Blast
#searchSimple Bio::DDBJ::REST::Blast
#searchSimpleAsync Bio::DDBJ::REST::Blast
#search_all Bio::FlatFileIndex::DataBank
#search_all_get_unique_id Bio::FlatFileIndex::DataBank
search_database_list Bio::TogoWS::REST
#search_database_list Bio::TogoWS::REST
#search_names Bio::FlatFileIndex::NameSpaces
#search_namespaces Bio::FlatFileIndex::DataBank
#search_namespaces Bio::FlatFileIndex
#search_namespaces_get_unique_id Bio::FlatFileIndex::DataBank
#search_primary Bio::FlatFileIndex::DataBank
#search_primary Bio::FlatFileIndex
#search_primary_get_unique_id Bio::FlatFileIndex::DataBank
#secondary Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#secondary Bio::FlatFileIndex::DataBank
#secondary= Bio::FlatFileIndex::DataBank
#secondary_accessions Bio::Sequence
#secondary_ids Bio::Sequence::DBLink
#secondary_namespaces Bio::FlatFileIndex
#seek Bio::FlatFileIndex::Flat_1::FlatMappingFile
#seek Bio::FlatFileIndex::FileID
#segment Bio::NCBIDB::Common
#segmentpairs Bio::Spidey::Report::Hit
#segmentpairs Bio::Sim4::Report::Hit
#segments Bio::DAS::GFF
#segments Bio::DAS::ENTRY_POINT
#select Bio::Alignment::OriginalAlignment
#sense Bio::SiRNA::Pair
#seq Bio::GenPept
#seq Bio::GenBank
#seq Bio::SQL::Sequence
#seq Bio::Spidey::Report::Segment
#seq Bio::SangerChromatogram
#seq Bio::PSORT::PSORT2::Report
#seq Bio::Sim4::Report::Segment
#seq Bio::Sequence::Common
#seq Bio::Lasergene
#seq Bio::SPTR
#seq Bio::EMBL
#seq Bio::GCG::Seq
#seq Bio::Sequence
seq Bio::DBGET
#seq Bio::Fastq
#seq Bio::FastaFormat
#seq Bio::NBRF
#seq1 Bio::Sim4::Report::Hit
#seq1 Bio::Sim4::Report::SegmentPair
#seq1 Bio::Sim4::Report
seq1_intron Bio::Sim4::Report::SegmentPair
#seq2 Bio::Sim4::Report::Hit
#seq2 Bio::Sim4::Report::SegmentPair
seq2 Bio::DBGET
seq2_intron Bio::Sim4::Report::SegmentPair
#seq= Bio::SQL::Sequence
#seq_class Bio::NBRF
#seq_data Bio::GCG::Msf
#seq_f Bio::HMMER::Report::Hsp
#seq_ft Bio::HMMER::Report::Hsp
#seq_len Bio::GenPept
#seq_len Bio::GenBank
#seq_t Bio::HMMER::Report::Hsp
#seq_type Bio::GCG::Seq
#seq_type Bio::GCG::Msf
#seq_type Bio::NBRF
#seqclass Bio::MAFFT::Report
#seqclass Bio::ClustalW::Report
#seqclass Bio::Alignment::EnumerableExtension
#seqclass Bio::Alignment::PropertyMethods
#seqfile Bio::HMMER
#seqid Bio::GFF::GFF3::SequenceRegion
#seqname Bio::GFF::Record
#seqres Bio::PDB
seqret Bio::EMBOSS
#seqs Bio::Blat::Report::SeqDesc
#sequence Bio::Fasta::Report::Hit::Query
#sequence Bio::SOSUI::Report::TMH
#sequence Bio::PSORT::PSORT1::Report
#sequence Bio::Lasergene
#sequence Bio::NCBI::REST::EFetch::Methods
#sequence Bio::Shell::Demo
#sequence Bio::PSORT::PSORT1
#sequence Bio::FANTOM::MaXML::Cluster
#sequence Bio::Location
#sequence Bio::SangerChromatogram
#sequence Bio::SQL::Seqfeature
#sequence Bio::DAS::SEQUENCE
#sequence Bio::DAS::DNA
#sequence Bio::SQL::Location
#sequence_length Bio::SPTR
#sequence_length Bio::EMBL
#sequence_name Bio::Meme::Motif
#sequence_names Bio::Alignment::HashExtension
#sequence_names Bio::Alignment::EnumerableExtension
#sequence_position Bio::Reference
#sequence_regions Bio::GFF::GFF3
#sequence_relations Bio::PhyloXML::Tree
#sequence_string Bio::SangerChromatogram
#sequence_string Bio::Fastq
#sequence_version Bio::Sequence
#sequences Bio::PhyloXML::Node
#sequences Bio::FANTOM::MaXML::Cluster
#sequences Bio::GFF::GFF3
#serial Bio::PDB::Model
#series Bio::SOFT
#server Bio::Ensembl
#server Bio::Fasta
#server Bio::Blast
server_uri Bio::Ensembl
#session_dir Bio::Shell::Core
#set Bio::Blast::NCBIOptions
#set_RN Bio::SPTR
#set_aaseq Bio::Genscan::Report::Gene
#set_alignment Bio::HMMER::Report::Hsp
#set_all_property Bio::Alignment::PropertyMethods
#set_attribute Bio::GFF::GFF2::Record
#set_cut_symbol Bio::RestrictionEnzyme::CutSymbol
#set_datatype Bio::Nexus::CharactersBlock
#set_date Bio::GO::External2go
#set_default_parameters Bio::PAML::Common
#set_desc Bio::GO::External2go
#set_features Bio::PSORT::PSORT2::Report
#set_gap_character Bio::Nexus::CharactersBlock
#set_header_line Bio::PSORT::PSORT2::Report
set_kNN_prob Bio::PSORT::PSORT2::Report
#set_match_character Bio::Nexus::CharactersBlock
#set_matrix Bio::Nexus::DistancesBlock
#set_matrix Bio::Nexus::CharactersBlock
#set_missing Bio::Nexus::CharactersBlock
#set_naseq Bio::Genscan::Report::Gene
#set_number_of_characters Bio::Nexus::DistancesBlock
#set_number_of_characters Bio::Nexus::CharactersBlock
#set_number_of_taxa Bio::Nexus::DistancesBlock
#set_number_of_taxa Bio::Nexus::CharactersBlock
#set_number_of_taxa Bio::Nexus::TaxaBlock
#set_polyA Bio::Genscan::Report::Gene
#set_prediction Bio::PSORT::PSORT2::Report
#set_primary_namespace Bio::FlatFileIndex::Indexer::Parser::TemplateParser
#set_promoter Bio::Genscan::Report::Gene
#set_triangle Bio::Nexus::DistancesBlock
#set_value Bio::Nexus::NexusMatrix
#setup_colors Bio::Shell::ColoredCodonTable
#setup_irb Bio::Shell::Irb
#setup_savedir Bio::Shell::Setup
#sf Bio::TRANSFAC::FACTOR
#sf Bio::TRANSFAC::SITE
#shape Bio::KEGG::KGML::Entry
#shape= Bio::KEGG::KGML::Entry
#sheet Bio::PDB
#shell Bio::Shell::Demo
#shell_dir Bio::Shell::Core
#shift Bio::Alignment::OriginalAlignment
#sigatm Bio::PDB::Record::ATOM
#significant Bio::PAML::Codeml::Report
#siguij Bio::PDB::Record::ANISOU
#site Bio::PROSITE
#sites Bio::PAML::Codeml::Report
#size Bio::FlatFileIndex::Flat_1::Record
#size Bio::FlatFileIndex::Results
#size Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
#size Bio::Blat::Report::SeqDesc
#size Bio::RestrictionEnzyme::SortedNumArray
#size Bio::Alignment::OriginalAlignment
#size Bio::Hinv::KeywordSearch
#size Bio::RestrictionEnzyme::DenseIntArray
#size Bio::RestrictionEnzyme::Range::SequenceRange
#size Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#skip String
#skip_flag Bio::PROSITE
#skip_leader Bio::Fasta::Report::FastaFormat10Splitter
#skip_leader Bio::Blast::RPSBlast::RPSBlastSplitter
#skip_leader Bio::Blast::Report::BlastXmlSplitter
#skip_leader Bio::FlatFile::Splitter::Template
#skip_leader Bio::FlatFile::Splitter::Default
#skip_leader Bio::FlatFile::Splitter::LineOriented
#skip_leader_mode Bio::FlatFile
#skip_spaces Bio::FlatFile::BufferedInputStream
#small_world Bio::Pathway
#so Bio::TRANSFAC::SITE
#so Bio::MEDLINE
#solexa_p2q Bio::Sequence::QualityScore::Solexa
#solexa_q2p Bio::Sequence::QualityScore::Solexa
#solvents Bio::PDB::Model
#sort! Bio::RestrictionEnzyme::SortedNumArray
#sort! Bio::RestrictionEnzyme::DenseIntArray
#sort_attributes_by_tag! Bio::GFF::GFF2::Record
#source Bio::PhyloXML::Accession
#source Bio::NCBIDB::Common
#source Bio::PhyloXML::Annotation
#source Bio::DAS::DSN
#source Bio::GFF::Record
#source_id Bio::DAS::DSN
#source_version Bio::DAS::DSN
#span Bio::Locations
#spec_version Bio::Registry
#speciations Bio::PhyloXML::Events
#species Bio::EMBL
#species Bio::Sequence
#splash_message Bio::Shell::Ghost
#splash_message_action Bio::Shell::Ghost
#splash_message_action_color Bio::Shell::Ghost
#splash_message_color Bio::Shell::Ghost
#splice Bio::Sequence::Common
#splice_site Bio::Spidey::Report::SegmentPair
#splicing Bio::Sequence::NA
#sppta Bio::PTS1::Report
#spptna Bio::PTS1::Report
#sq Bio::SPTR
#sq Bio::EMBL
#sq Bio::TRANSFAC::FACTOR
#sq Bio::TRANSFAC::SITE
#ssbond Bio::PDB
#st Bio::TRANSFAC::SITE
#standard_comment? Bio::Lasergene
#start Bio::Fasta::Report::Hit::Query
#start Bio::Blat::Report::SeqDesc
#start Bio::CodonTable
#start Bio::SiRNA::Pair
#start Bio::KEGG::API
#start Bio::Hinv::KeywordSearch
#start Bio::DAS::TARGET
#start Bio::DAS::FEATURE
#start Bio::DAS::SEQUENCE
#start Bio::DAS::DNA
#start Bio::DAS::SEGMENT
#start Bio::GFF::GFF3::Record::Target
#start Bio::GFF::GFF3::SequenceRegion
#start Bio::GFF::Record
#start_codon? Bio::CodonTable
start_http Bio::Command
#start_irb Bio::Shell::Irb
#start_pos Bio::Meme::Motif
#starts Bio::Blat::Report::SeqDesc
#stat_method Bio::Blast::Default::Report::HSP
#statistical_detail Bio::HMMER::Report
#statistics Bio::Blast::Report::Iteration
#statistics Bio::Blast::Report
#statistics Bio::KEGG::GENOME
#status Bio::Iprscan::Report::Match
#status Bio::TMHMM::TMH
#step String
#sticky? Bio::RestrictionEnzyme::DoubleStranded
#stop Bio::Fasta::Report::Hit::Query
#stop Bio::CodonTable
#stop Bio::SiRNA::Pair
#stop Bio::DAS::TARGET
#stop Bio::DAS::FEATURE
#stop Bio::DAS::SEQUENCE
#stop Bio::DAS::DNA
#stop Bio::DAS::SEGMENT
#stop_codon? Bio::CodonTable
#store Bio::Shell::Web::Results
#store Bio::Alignment::OriginalAlignment
#store_history Bio::Shell::Ghost
#str2scores Bio::Fastq::FormatData
#strand Bio::Genscan::Report::Exon
#strand Bio::GenBank
#strand Bio::GenBank::Locus
#strand Bio::Spidey::Report::Hit
#strand Bio::Spidey::Report::Segment
#strand Bio::Blat::Report::Hit
#strand Bio::Meme::Motif
#strand Bio::Location
#strand Bio::GFF::GFF3::Record::Target
#strand Bio::GFF::Record
#strandedness Bio::GenBank
#strandedness Bio::Sequence
#strands_for_display Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#strands_for_display_current Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#strip Bio::Alignment::OriginalAlignment
#strip_cuts_and_padding Bio::RestrictionEnzyme::StringFormatting
#strip_padding Bio::RestrictionEnzyme::StringFormatting
#stripped Bio::RestrictionEnzyme::SingleStrand
#structure Bio::KEGG::GENES
#structure Bio::PDB::Model
#structures Bio::KEGG::ENZYME
#subgraph Bio::Pathway
#subparts Bio::DAS::SEGMENT
#subseq Bio::Sequence::Common
#subsets Bio::SOFT
#substrates Bio::KEGG::ENZYME
#substrates Bio::KEGG::KGML::Reaction
#subtree Bio::Tree
#subtree_with_all_paths Bio::Tree
#supplemental_outputs Bio::PAML::Common
supplier_data= Bio::REBASE::EnzymeEntry
#supplier_names Bio::REBASE::EnzymeEntry
#sv Bio::EMBL
#sw Bio::Fasta::Report::Hit
#swissprot_release_number Bio::PROSITE
#swissprot_release_sequences Bio::PROSITE
#sy Bio::TRANSFAC::FACTOR
#symbol Bio::PhyloXML::Sequence
#symbol Bio::Fastq::FormatData
#symbol_comparison_table Bio::GCG::Msf
symbols Bio::PDB::Record
#synonyms Bio::SPTR
#synonyms Bio::Taxonomy
#sysname Bio::KEGG::ENZYME
#sz Bio::TRANSFAC::FACTOR
#t_score Bio::Genscan::Report::Exon
#ta Bio::MEDLINE
tab Bio::Blast::Report
#table Bio::Shell::ColoredCodonTable
#table Bio::CodonTable
#table Bio::ContingencyTable
#tag_number Bio::Abif::DirectoryEntry
#tags Bio::DB
#target Bio::Fasta::Report::Hit
#target Bio::Blat::Report::Hit
#target Bio::SiRNA::Pair
#target_avg Bio::KEGG::EXPRESSION
#target_def Bio::Fasta::Report::Hit
#target_def Bio::Spidey::Report::Hit
#target_def Bio::HMMER::Report::Hit
#target_def Bio::Sim4::Report::Hit
#target_def Bio::Blat::Report::Hit
#target_end Bio::Fasta::Report::Hit
#target_end Bio::Blast::Default::Report::Hit
#target_end Bio::Blast::Report::Hit
#target_frame Bio::HMMER::Report::Hsp
#target_from Bio::HMMER::Report::Hsp
#target_id Bio::Fasta::Report::Hit
#target_id Bio::Spidey::Report::Hit
#target_id Bio::Blast::Default::Report::Hit
#target_id Bio::Sim4::Report::Hit
#target_id Bio::GFF::GFF3::Record::Target
#target_len Bio::Fasta::Report::Hit
#target_len Bio::Spidey::Report::Hit
#target_len Bio::Sim4::Report::Hit
#target_len Bio::Blat::Report::Hit
#target_sd Bio::KEGG::EXPRESSION
#target_seq Bio::Fasta::Report::Hit
#target_seq Bio::Blast::Default::Report::Hit
#target_seq Bio::HMMER::Report::Hsp
#target_seq Bio::Blast::Report::Hit
#target_start Bio::Fasta::Report::Hit
#target_start Bio::Blast::Default::Report::Hit
#target_start Bio::Blast::Report::Hit
#target_to Bio::HMMER::Report::Hsp
#target_type Bio::Fasta::Report::Hit
#target_var Bio::KEGG::EXPRESSION
#targets Bio::DAS::GROUP
#targets Bio::DAS::FEATURE
#taxa_list Bio::KEGG::Keggtab
#taxid Bio::KEGG::GENOME
#taxo2korgs Bio::KEGG::Keggtab
#taxon Bio::GO::GeneAssociation
#taxon_range Bio::PROSITE
#taxonomies Bio::PhyloXML::Node
#taxonomy Bio::SQL::Sequence
#taxonomy Bio::NCBIDB::Common
#taxonomy Bio::KEGG::Keggtab
#taxonomy Bio::KEGG::GENOME
#taxonomy Bio::NCBI::REST::EFetch::Methods
#taxonomy_id Bio::PhyloXML::Taxonomy
#taxonomy_id Bio::Tree::Node
#ter Bio::PDB::Record::ATOM
#text Bio::DAS::LINK
#three2name Bio::AminoAcid::Data
#three2one Bio::AminoAcid::Data
#threshold Bio::Fasta::Report
#ti Bio::MEDLINE
#time Bio::Genscan::Report
#title Bio::PSORT::PSORT1::Report
#title Bio::KEGG::KGML
#title Bio::AAindex
#title Bio::PSORT::PSORT1::Remote
#title Bio::PSORT::PSORT1
#title Bio::PSORT::PSORT2
#title Bio::Reference
#title Bio::LITDB
#tmhs Bio::TMHMM::Report
#tmhs Bio::SOSUI::Report
#to Bio::Spidey::Report::Segment
#to Bio::Sim4::Report::Segment
#to Bio::PhyloXML::ProteinDomain
#to Bio::Location
#to Bio::Relation
#to_1 Bio::AminoAcid::Data
#to_3 Bio::AminoAcid::Data
#to_a Bio::MAFFT::Report
to_a Bio::FlatFile
#to_a Bio::PDB::Record::ATOM
#to_a Bio::FANTOM::MaXML::Annotations
#to_a Bio::FANTOM::MaXML::Sequences
#to_a Bio::RestrictionEnzyme::SortedNumArray
#to_a Bio::PAML::Codeml::PositiveSite
#to_a Bio::ClustalW::Report
#to_aaseq String
#to_array_index Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
#to_array_index Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
#to_ary Bio::PDB::Coordinate
#to_biosequence Bio::GenBank
#to_biosequence Bio::SQL::Sequence
#to_biosequence Bio::FastaNumericFormat
#to_biosequence Bio::EMBL
#to_biosequence Bio::PhyloXML::Sequence
#to_biosequence Bio::Fastq
#to_biosequence Bio::FastaFormat
#to_biosequence Bio::SangerChromatogram
#to_biosql Bio::SQL::Sequence
#to_biotreenode Bio::PhyloXML::Node
#to_clustal Bio::Alignment::Output
#to_fasta Bio::SQL::Sequence
#to_fasta Bio::MAFFT::Report
#to_fasta Bio::Sequence::Common
#to_fasta Bio::Alignment::OriginalAlignment
#to_fasta Bio::ClustalW::Report
#to_fasta_array Bio::Alignment::OriginalAlignment
#to_fasta_reverse_complememt Bio::SQL::Sequence
#to_fastaformat_array Bio::Alignment::OriginalAlignment
to_gcg Bio::GCG::Seq
#to_hash Bio::Iprscan::Report
#to_hash Bio::Alignment::OriginalAlignment
#to_hash Bio::Feature
#to_io Bio::FlatFile::BufferedInputStream
#to_io Bio::FlatFile
#to_list Bio::Pathway
#to_matrix Bio::Pathway
#to_midi Bio::Sequence::NA
#to_naseq String
to_nbrf Bio::NBRF
#to_nexus Bio::Nexus::TreesBlock
#to_nexus Bio::Nexus::DistancesBlock
#to_nexus Bio::Nexus::CharactersBlock
#to_nexus Bio::Nexus::DataBlock
#to_nexus Bio::Nexus::GenericBlock
#to_nexus Bio::Nexus::TaxaBlock
to_nexus_helper Bio::Nexus::Util
#to_nexus_row_array Bio::Nexus::NexusMatrix
#to_re Bio::Sequence::NA
#to_re Bio::Sequence::AA
#to_re Bio::NucleicAcid::Data
#to_re Bio::AminoAcid::Data
#to_relations Bio::Pathway
#to_s Bio::Blast::Default::Report
#to_s Bio::FlatFileIndex::DataBank
#to_s Bio::FlatFileIndex::NameSpaces
#to_s Bio::FlatFileIndex::Flat_1::Record
#to_s Bio::FlatFileIndex::FileID
#to_s Bio::FlatFileIndex::Results
#to_s Bio::TMHMM::Report
#to_s Bio::TMHMM::TMH
#to_s Bio::FastaDefline
#to_s Bio::Sequence
#to_s Bio::Sequence::Common
#to_s Bio::PDB::Residue
#to_s Bio::PDB::Model
#to_s Bio::PDB::Chain
#to_s Bio::PDB
#to_s Bio::PDB::Record::ATOM
#to_s Bio::FANTOM::MaXML
#to_s Bio::Locations
#to_s Bio::Nexus::NexusMatrix
#to_s Bio::Nexus::GenericBlock
#to_s Bio::Nexus
#to_s Bio::Fastq
#to_s Bio::GFF::GFF3::RecordBoundary
#to_s Bio::GFF::GFF3::Record::Gap
#to_s Bio::GFF::GFF3::Record::Target
#to_s Bio::GFF::GFF3::Record::Gap::Code
#to_s Bio::GFF::GFF3::Record
#to_s Bio::GFF::GFF3::SequenceRegion
#to_s Bio::GFF::GFF3
#to_s Bio::GFF::GFF2::Record
#to_s Bio::GFF::GFF2::MetaData
#to_s Bio::GFF::GFF2
#to_s Bio::GFF::GFF2::Record::Value
#to_s Bio::Tree::Node
#to_s Bio::Tree::Edge
#to_s Bio::SQL::Location
#to_s Bio::PAML::Codeml::PositiveSites
#to_s Bio::PAML::Codeml::Model
#to_s Bio::PhyloXML::Date
#to_str Bio::GO::External2go
#to_str Bio::GO::GeneAssociation
to_string Bio::FlatFileIndex::Flat_1::Record
#to_xml Bio::PhyloXML::CladeRelation
#to_xml Bio::PhyloXML::Property
#to_xml Bio::PhyloXML::Reference
#to_xml Bio::PhyloXML::Other
#to_xml Bio::PhyloXML::SequenceRelation
#to_xml Bio::PhyloXML::ProteinDomain
#to_xml Bio::PhyloXML::DomainArchitecture
#to_xml Bio::PhyloXML::Date
#to_xml Bio::PhyloXML::BinaryCharacters
#to_xml Bio::PhyloXML::Id
#to_xml Bio::PhyloXML::BranchColor
#to_xml Bio::PhyloXML::Annotation
#to_xml Bio::PhyloXML::Uri
#to_xml Bio::PhyloXML::Accession
#to_xml Bio::PhyloXML::Sequence
#to_xml Bio::PhyloXML::Point
#to_xml Bio::PhyloXML::Polygon
#to_xml Bio::PhyloXML::Confidence
#to_xml Bio::PhyloXML::Events
#to_xml Bio::PhyloXML::Distribution
#to_xml Bio::PhyloXML::Node
#to_xml Bio::PhyloXML::Taxonomy
to_xyz Bio::PDB::Utils
too_short_parser Bio::PSORT::PSORT2::Report
#top_strand Bio::SiRNA::ShRNA
#top_strand_sequences Bio::Lasergene
#topology Bio::EMBL
#topology Bio::Sequence
#total Bio::Sequence::Common
#total Bio::PROSITE
#total_distance Bio::Tree
#total_hits Bio::PROSITE
#total_length Bio::Lasergene
#total_prob_of_N_in Bio::TMHMM::Report
#total_seq_searched Bio::HMMER::Report
#total_sequences Bio::Lasergene
#total_sequences Bio::PROSITE
#tqual Bio::Scf
#tr Bio::TRANSFAC::GENE
#translate Bio::Sequence::NA
#translate Bio::SQL::Seqfeature
#tree Bio::Newick
#tree Bio::PAML::Codeml::Model
#tree Bio::PAML::Codeml::ReportSingle
#tree Bio::PAML::Codeml::Report
#tree_length Bio::PAML::Codeml::Model
#tree_length Bio::PAML::Codeml::ReportSingle
#tree_length Bio::PAML::Codeml::Report
#tree_log_likelihood Bio::PAML::Codeml::Report
#tree_log_likelihood Bio::PAML::Codeml::ReportSingle
#trends Bio::Reference
#tsort_each_child Bio::FlatFile::AutoDetect
#tsort_each_node Bio::FlatFile::AutoDetect
#ttrace Bio::SangerChromatogram
#turn Bio::PDB
#tutorial Bio::Shell::Demo
#ty Bio::TRANSFAC::SITE
#type Bio::KEGG::Keggtab::DB
#type Bio::KEGG::KGML::Reaction
#type Bio::KEGG::KGML::Relation
#type Bio::KEGG::KGML::Graphics
#type Bio::KEGG::KGML::Entry
#type Bio::DAS::GROUP
#type Bio::Map::SimpleMap
#type Bio::PhyloXML::SequenceRelation
#type Bio::PhyloXML::CladeRelation
#type Bio::PhyloXML::Annotation
#type Bio::PhyloXML::Uri
#type Bio::PhyloXML::Confidence
#type Bio::PhyloXML::Events
#type Bio::PhyloXML::Sequence
#type Bio::PhyloXML::Tree
#types Bio::DAS::FEATURE
#types Bio::DAS::SEGMENT
#ui Bio::MEDLINE
#uitei Bio::SiRNA
#uitei? Bio::SiRNA
#undirected Bio::Pathway
#undirected? Bio::Pathway
ungapped_pos Bio::Alignment::GAP
#ungetc Bio::FlatFile::BufferedInputStream
#ungets Bio::FlatFile::BufferedInputStream
#uniq! Bio::RestrictionEnzyme::SortedNumArray
#uniq! Bio::RestrictionEnzyme::DenseIntArray
#unit Bio::PhyloXML::Property
#unit Bio::PhyloXML::Date
#units Bio::Map::SimpleMap
#unknown Bio::PROSITE
#unknown_hits Bio::PROSITE
#unknown_sequences Bio::PROSITE
#unshift Bio::Alignment::OriginalAlignment
#unshift Bio::RestrictionEnzyme::SortedNumArray
#unshift Bio::RestrictionEnzyme::DenseIntArray
#up_regulated Bio::KEGG::EXPRESSION
update_index Bio::FlatFileIndex
update_index Bio::FlatFileIndex::Indexer
#uri Bio::PhyloXML::Annotation
#uri Bio::PhyloXML::Uri
#uri Bio::PhyloXML::Sequence
#uri Bio::PhyloXML::Taxonomy
#url Bio::Reference
v_parser Bio::PSORT::PSORT2::Report
#val Bio::FlatFileIndex::Flat_1::Record
#val2rgb Bio::KEGG::EXPRESSION
#validate_checksum Bio::GCG::Seq
#validate_checksum Bio::GCG::Msf
#validate_format Bio::Fastq
#value Bio::KEGG::KGML::Relation
#value Bio::Feature::Qualifier
#value Bio::PhyloXML::Other
#value Bio::PhyloXML::Property
#value Bio::PhyloXML::ProteinDomain
#value Bio::PhyloXML::Date
#value Bio::PhyloXML::Id
#value Bio::PhyloXML::Accession
#value Bio::PhyloXML::Confidence
#values Bio::Alignment::OriginalAlignment
#values Bio::GFF::GFF2::Record::Value
#vc_complement Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#vc_complement_as_original_class Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#vc_primary Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#vc_primary_as_original_class Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
#version Bio::TargetP::Report
#version Bio::SQL::Sequence
#version Bio::Blast::Default::Report
#version Bio::NCBIDB::Common
#version Bio::TMHMM::TMH
#version Bio::Blast::Report
#version Bio::EMBL
#version Bio::PDB
version Bio::DBGET
#version Bio::DAS::GFF
#version Bio::DAS::SEQUENCE
#version Bio::DAS::DNA
#version Bio::DAS::SEGMENT
#version Bio::DAS::ENTRY_POINT
#version Bio::SangerChromatogram
#version= Bio::SQL::Sequence
#version_date Bio::Blast::Default::Report
#version_number Bio::Blast::Default::Report
#versions Bio::NCBIDB::Common
#vi Bio::MEDLINE
#volume Bio::Reference
#volume Bio::LITDB
#wait_getAsyncResult Bio::DDBJ::REST::RequestManager
wait_getAsyncResult Bio::DDBJ::REST::RequestManager
#warnings Bio::Blast::WU::Report::Iteration
#warnings Bio::Blast::WU::Report
#weight Bio::NucleicAcid::Data
#weight Bio::AminoAcid::Data
#whole_seq_top_hits Bio::HMMER::Report
#width Bio::KEGG::KGML::Entry
#width Bio::KEGG::KGML::Graphics
#width Bio::Tree::Edge
#width Bio::PhyloXML::Node
#width= Bio::KEGG::KGML::Entry
#window_search Bio::Sequence::Common
#with Bio::GO::GeneAssociation
#with_cut_symbols Bio::RestrictionEnzyme::SingleStrand
#with_spaces Bio::RestrictionEnzyme::SingleStrand
#words Bio::FastaDefline
#write Bio::FlatFileIndex::DataBank
#write Bio::PhyloXML::Writer
#write_branch_length_as_subelement Bio::PhyloXML::Writer
#write_other Bio::PhyloXML::Writer
#write_record Bio::FlatFileIndex::Flat_1::FlatMappingFile
#writeback_array Bio::FlatFileIndex::BDBwrapper
#wsdl Bio::SOAPWSDL
#x Bio::KEGG::KGML::Graphics
#x Bio::KEGG::KGML::Entry
#x Bio::PDB::Coordinate
#x= Bio::KEGG::KGML::Entry
#x= Bio::PDB::Coordinate
xmlparser Bio::Blast::Report
#xref_id Bio::Location
#xyz Bio::PDB::Coordinate
#xyz Bio::PDB::Record::ATOM
#y Bio::KEGG::KGML::Graphics
#y Bio::KEGG::KGML::Entry
#y Bio::PDB::Coordinate
#y= Bio::KEGG::KGML::Entry
#y= Bio::PDB::Coordinate
#year Bio::MEDLINE
#year Bio::Reference
#z Bio::PDB::Coordinate
#z= Bio::PDB::Coordinate