### Home Classes Methods

### In Files

- lib/bio/tree/output.rb
- lib/bio/io/sql.rb
- lib/bio/io/hinv.rb
- lib/bio/io/togows.rb
- lib/bio/io/ddbjxml.rb
- lib/bio/io/soapwsdl.rb
- lib/bio/io/ncbirest.rb
- lib/bio/io/flatfile/autodetection.rb
- lib/bio/io/flatfile/indexer.rb
- lib/bio/io/flatfile/buffer.rb
- lib/bio/io/flatfile/splitter.rb
- lib/bio/io/flatfile/index.rb
- lib/bio/io/flatfile/bdb.rb
- lib/bio/io/pubmed.rb
- lib/bio/io/biosql/ar-biosql.rb
- lib/bio/io/biosql/biosql.rb
- lib/bio/io/ebisoap.rb
- lib/bio/io/registry.rb
- lib/bio/io/fetch.rb
- lib/bio/io/flatfile.rb
- lib/bio/io/fastacmd.rb
- lib/bio/io/das.rb
- lib/bio/io/dbget.rb
- lib/bio/io/keggapi.rb
- lib/bio/io/ensembl.rb
- lib/bio/io/ddbjrest.rb
- lib/bio/io/higet.rb
- lib/bio/io/ncbisoap.rb
- lib/bio/util/restriction_enzyme/string_formatting.rb
- lib/bio/util/restriction_enzyme/single_strand.rb
- lib/bio/util/restriction_enzyme/cut_symbol.rb
- lib/bio/util/restriction_enzyme/single_strand_complement.rb
- lib/bio/util/restriction_enzyme/range/cut_range.rb
- lib/bio/util/restriction_enzyme/range/sequence_range.rb
- lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
- lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
- lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
- lib/bio/util/restriction_enzyme/range/cut_ranges.rb
- lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/dense_int_array.rb
- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
- lib/bio/util/restriction_enzyme/analysis_basic.rb
- lib/bio/util/restriction_enzyme/double_stranded.rb
- lib/bio/util/restriction_enzyme/sorted_num_array.rb
- lib/bio/util/restriction_enzyme/analysis.rb
- lib/bio/util/color_scheme.rb
- lib/bio/util/sirna.rb
- lib/bio/util/contingency_table.rb
- lib/bio/util/restriction_enzyme.rb
- lib/bio/db.rb
- lib/bio/sequence/compat.rb
- lib/bio/sequence/sequence_masker.rb
- lib/bio/sequence/dblink.rb
- lib/bio/sequence/quality_score.rb
- lib/bio/sequence/generic.rb
- lib/bio/sequence/na.rb
- lib/bio/sequence/format.rb
- lib/bio/sequence/common.rb
- lib/bio/sequence/adapter.rb
- lib/bio/sequence/aa.rb
- lib/bio/shell/plugin/das.rb
- lib/bio/reference.rb
- lib/bio/alignment.rb
- lib/bio/feature.rb
- lib/bio/version.rb
- lib/bio/tree.rb
- lib/bio/appl/bl2seq/report.rb
- lib/bio/appl/clustalw.rb
- lib/bio/appl/gcg/seq.rb
- lib/bio/appl/gcg/msf.rb
- lib/bio/appl/blat/report.rb
- lib/bio/appl/genscan/report.rb
- lib/bio/appl/psort.rb
- lib/bio/appl/fasta.rb
- lib/bio/appl/pts1.rb
- lib/bio/appl/sim4/report.rb
- lib/bio/appl/blast/format8.rb
- lib/bio/appl/blast/remote.rb
- lib/bio/appl/blast/xmlparser.rb
- lib/bio/appl/blast/rpsblast.rb
- lib/bio/appl/blast/wublast.rb
- lib/bio/appl/blast/report.rb
- lib/bio/appl/blast/ncbioptions.rb
- lib/bio/appl/blast/rexml.rb
- lib/bio/appl/blast/format0.rb
- lib/bio/appl/clustalw/report.rb
- lib/bio/appl/mafft.rb
- lib/bio/appl/iprscan/report.rb
- lib/bio/appl/psort/report.rb
- lib/bio/appl/sosui/report.rb
- lib/bio/appl/fasta/format10.rb
- lib/bio/appl/tcoffee.rb
- lib/bio/appl/phylip/alignment.rb
- lib/bio/appl/phylip/distance_matrix.rb
- lib/bio/appl/probcons.rb
- lib/bio/appl/emboss.rb
- lib/bio/appl/spidey/report.rb
- lib/bio/appl/hmmer/report.rb
- lib/bio/appl/paml/common.rb
- lib/bio/appl/paml/codeml.rb
- lib/bio/appl/sim4.rb
- lib/bio/appl/targetp/report.rb
- lib/bio/appl/muscle.rb
- lib/bio/appl/tmhmm/report.rb
- lib/bio/appl/mafft/report.rb
- lib/bio/appl/blast.rb
- lib/bio/appl/meme/motif.rb
- lib/bio/appl/meme/mast/report.rb
- lib/bio/appl/meme/mast.rb
- lib/bio/appl/hmmer.rb
- lib/bio/pathway.rb
- lib/bio/db/biosql/sequence.rb
- lib/bio/db/litdb.rb
- lib/bio/db/fasta.rb
- lib/bio/db/prosite.rb
- lib/bio/db/fasta/qual.rb
- lib/bio/db/fasta/defline.rb
- lib/bio/db/nbrf.rb
- lib/bio/db/aaindex.rb
- lib/bio/db/transfac.rb
- lib/bio/db/fantom.rb
- lib/bio/db/kegg/genes.rb
- lib/bio/db/kegg/pathway.rb
- lib/bio/db/kegg/taxonomy.rb
- lib/bio/db/kegg/reaction.rb
- lib/bio/db/kegg/keggtab.rb
- lib/bio/db/kegg/enzyme.rb
- lib/bio/db/kegg/compound.rb
- lib/bio/db/kegg/brite.rb
- lib/bio/db/kegg/kgml.rb
- lib/bio/db/kegg/genome.rb
- lib/bio/db/kegg/glycan.rb
- lib/bio/db/kegg/drug.rb
- lib/bio/db/kegg/common.rb
- lib/bio/db/kegg/expression.rb
- lib/bio/db/kegg/module.rb
- lib/bio/db/kegg/orthology.rb
- lib/bio/db/pdb/pdb.rb
- lib/bio/db/pdb/residue.rb
- lib/bio/db/pdb/utils.rb
- lib/bio/db/pdb/chain.rb
- lib/bio/db/pdb/atom.rb
- lib/bio/db/pdb/chemicalcomponent.rb
- lib/bio/db/pdb/model.rb
- lib/bio/db/gff.rb
- lib/bio/db/sanger_chromatogram/chromatogram.rb
- lib/bio/db/sanger_chromatogram/abif.rb
- lib/bio/db/sanger_chromatogram/scf.rb
- lib/bio/db/genbank/refseq.rb
- lib/bio/db/genbank/genpept.rb
- lib/bio/db/genbank/genbank.rb
- lib/bio/db/genbank/ddbj.rb
- lib/bio/db/genbank/common.rb
- lib/bio/db/fastq.rb
- lib/bio/db/pdb.rb
- lib/bio/db/nexus.rb
- lib/bio/db/medline.rb
- lib/bio/db/phyloxml/phyloxml_elements.rb
- lib/bio/db/phyloxml/phyloxml_parser.rb
- lib/bio/db/phyloxml/phyloxml_writer.rb
- lib/bio/db/embl/swissprot.rb
- lib/bio/db/embl/common.rb
- lib/bio/db/embl/embl.rb
- lib/bio/db/embl/trembl.rb
- lib/bio/db/embl/sptr.rb
- lib/bio/db/embl/uniprot.rb
- lib/bio/db/lasergene.rb
- lib/bio/db/newick.rb
- lib/bio/db/rebase.rb
- lib/bio/db/soft.rb
- lib/bio/db/go.rb
- lib/bio/location.rb
- lib/bio/sequence.rb
- lib/bio/compat/references.rb
- lib/bio/compat/features.rb
- lib/bio/command.rb
- lib/bio/data/codontable.rb
- lib/bio/data/na.rb
- lib/bio/data/aa.rb
- lib/bio/map.rb
- lib/bio.rb

### Namespace

- MODULE Bio::Alignment
- MODULE Bio::ColorScheme
- MODULE Bio::Command
- MODULE Bio::FANTOM
- MODULE Bio::GCG
- MODULE Bio::Map
- MODULE Bio::Meme
- MODULE Bio::PAML
- MODULE Bio::Phylip
- MODULE Bio::PhyloXML
- MODULE Bio::Shell
- MODULE Bio::TogoWS
- CLASS Bio::AAindex
- CLASS Bio::AAindex1
- CLASS Bio::AAindex2
- CLASS Bio::Abif
- CLASS Bio::AminoAcid
- CLASS Bio::Blast
- CLASS Bio::Blat
- CLASS Bio::ClustalW
- CLASS Bio::CodonTable
- CLASS Bio::ContingencyTable
- CLASS Bio::DAS
- CLASS Bio::DB
- CLASS Bio::DBGET
- CLASS Bio::DDBJ
- CLASS Bio::EBI
- CLASS Bio::EMBL
- CLASS Bio::EMBLDB
- CLASS Bio::EMBOSS
- CLASS Bio::Ensembl
- CLASS Bio::Fasta
- CLASS Bio::FastaDefline
- CLASS Bio::FastaFormat
- CLASS Bio::FastaNumericFormat
- CLASS Bio::Fastq
- CLASS Bio::Feature
- CLASS Bio::Features
- CLASS Bio::Fetch
- CLASS Bio::FlatFile
- CLASS Bio::FlatFileIndex
- CLASS Bio::GFF
- CLASS Bio::GO
- CLASS Bio::GenBank
- CLASS Bio::GenPept
- CLASS Bio::Genscan
- CLASS Bio::HGC
- CLASS Bio::HMMER
- CLASS Bio::Hinv
- CLASS Bio::Iprscan
- CLASS Bio::KEGG
- CLASS Bio::KEGGDB
- CLASS Bio::LITDB
- CLASS Bio::Lasergene
- CLASS Bio::Location
- CLASS Bio::Locations
- CLASS Bio::MAFFT
- CLASS Bio::MEDLINE
- CLASS Bio::Muscle
- CLASS Bio::NBRF
- CLASS Bio::NCBI
- CLASS Bio::NCBIDB
- CLASS Bio::Newick
- CLASS Bio::Nexus
- CLASS Bio::NucleicAcid
- CLASS Bio::PDB
- CLASS Bio::PROSITE
- CLASS Bio::PSORT
- CLASS Bio::PTS1
- CLASS Bio::Pathway
- CLASS Bio::Probcons
- CLASS Bio::PubMed
- CLASS Bio::REBASE
- CLASS Bio::RefSeq
- CLASS Bio::Reference
- CLASS Bio::References
- CLASS Bio::Registry
- CLASS Bio::RestrictionEnzyme
- CLASS Bio::SOAPWSDL
- CLASS Bio::SOFT
- CLASS Bio::SOSUI
- CLASS Bio::SPTR
- CLASS Bio::SQL
- CLASS Bio::SangerChromatogram
- CLASS Bio::Scf
- CLASS Bio::Sequence
- CLASS Bio::SiRNA
- CLASS Bio::Sim4
- CLASS Bio::Spidey
- CLASS Bio::SwissProt
- CLASS Bio::TMHMM
- CLASS Bio::TRANSFAC
- CLASS Bio::TargetP
- CLASS Bio::Taxonomy
- CLASS Bio::Tcoffee
- CLASS Bio::TrEMBL
- CLASS Bio::Tree
- CLASS Bio::UniProt

### Methods

- ::method_missing

### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
- Bio::Blast::Remote::Ddbj
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::FLATFILE_SPLITTER
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FLATFILE_SPLITTER
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGG::Taxonomy
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBI::SOAP
- Bio::NCBI::SOAP::EFetch
- Bio::NCBI::SOAP::EFetchLite
- Bio::NCBI::SOAP::EUtils
- Bio::NCBI::SOAP::EUtilsLite
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::Edge
- Bio::Newick::Node
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
- Bio::PhyloXML::Annotation
- Bio::PhyloXML::BinaryCharacters
- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
- Bio::PhyloXML::Date
- Bio::PhyloXML::Distribution
- Bio::PhyloXML::DomainArchitecture
- Bio::PhyloXML::Events
- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
- Bio::PhyloXML::Other
- Bio::PhyloXML::Parser
- Bio::PhyloXML::Point
- Bio::PhyloXML::Polygon
- Bio::PhyloXML::Property
- Bio::PhyloXML::ProteinDomain
- Bio::PhyloXML::Reference
- Bio::PhyloXML::Sequence
- Bio::PhyloXML::SequenceRelation
- Bio::PhyloXML::Taxonomy
- Bio::PhyloXML::Tree
- Bio::PhyloXML::Uri
- Bio::PhyloXML::Writer
- Bio::Probcons
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SPTR
- Bio::SQL
- Bio::SQL::Biodatabase
- Bio::SQL::Bioentry
- Bio::SQL::BioentryDbxref
- Bio::SQL::BioentryPath
- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::NA::MidiTrack
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::Shell
- Bio::Shell::ColoredCodonTable
- Bio::Shell::Core
- Bio::Shell::Demo
- Bio::Shell::Ghost
- Bio::Shell::Irb
- Bio::Shell::Private
- Bio::Shell::Script
- Bio::Shell::Setup
- Bio::Shell::Web
- Bio::Shell::Web::Results
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio

# bio/tree/output.rb - Phylogenetic tree formatter

Copyright | Copyright (C) 2004-2006 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

## Description

This file contains formatter of Newick, NHX and Phylip distance matrix.

## References

- evolution.genetics.washington.edu/phylip/newick_doc.html

- www.phylosoft.org/forester/NHX.html

Ok Hilmar gives to me some clarification 1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.

    If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.

TODO: 1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized. 2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file. 3) Chk Locations in Biofeatures ArSQL

# bio/io/flatfile.rb - flatfile access wrapper class

    Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>

License | The Ruby License

    $Id:$

Bio::FlatFile is a helper and wrapper class to read a biological data file. It acts like a IO object. It can automatically detect data format, and users do not need to tell the class what the data is.

bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/horizontal_cut_range.rb -

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb -

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/sequence_range/fragment.rb -

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/analysis/fragments.rb -

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/range/vertical_cut_range.rb -

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/dense_int_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright | Copyright (C) 2011 Naohisa Goto <ng@bioruby.org> Tomoaki NISHIYAMA
License | The Ruby License

bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange

Copyright | Copyright (C) 2011 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

    $Id:$

bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

    $Id:$

bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

# bio/sequence/compat.rb - methods for backward compatibility

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>
License | The Ruby License

# bio/sequence/sequence_masker.rb - Sequence masking helper methods

Copyright | Copyright (C) 2010 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

## Description

Bio::Sequence::SequenceMasker is a mix-in module to provide helpful methods for masking a sequence.

For details, see documentation of Bio::Sequence::SequenceMasker.

# bio/sequence/dblink.rb - sequence ID with database name

Copyright | Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# bio/sequence/quality_score.rb - Sequence quality score manipulation modules

Copyright | Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

## Description

Sequence quality score manipulation modules, mainly used by Bio::Fastq and related classes.

## References

- FASTQ format specification maq.sourceforge.net/fastq.shtml

# bio/sequence/generic.rb - generic sequence class to store an intact string

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

# bio/sequence/na.rb - nucleic acid sequence class

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>
License | The Ruby License

# bio/sequence/common.rb - common methods for biological sequence

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>
License | The Ruby License

# bio/sequence/adapter.rb - Bio::Sequence adapter helper module

Copyright | Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>,
License | The Ruby License

# bio/sequence/aa.rb - amino acid sequence class

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>
License | The Ruby License

# bio/shell/plugin/keggdas.rb - plugin for KEGG DAS

Copyright | Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $

+

# bio/feature.rb - Features/Feature class (GenBank Feature table)

Copyright

Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>

    2006        Jan Aerts <jan.aerts@bbsrc.ac.uk>

License | The Ruby License

# bio/version.rb - BioRuby version information

Copyright | Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>, Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser

Copyright | Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.

# Acknowledgements

Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp> for providing bl2seq parser patches based on lib/bio/appl/blast/format0.rb.

# bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)

Copyright | Copyright (C) 2003, 2006 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

$Id: seq.rb,v 1.3 2007/04/05 23:35:39 trevor Exp $

# About Bio::GCG::Seq

Please refer document of Bio::GCG::Seq.

+

# bio/appl/sim4/report.rb - sim4 result parser

Copyright | Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
License | The Ruby License

    $Id:$

The sim4 report parser classes.

## References

- Florea, L., et al., A Computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Research, 8, 967--974, 1998. www.genome.org/cgi/content/abstract/8/9/967

# bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser

Copyright | Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

## Note

This file is automatically loaded by bio/appl/blast/report.rb

# bio/appl/blast/remote.rb - remote BLAST wrapper basic module

Copyright | Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# bio/appl/blast/wublast.rb - WU-BLAST default output parser

Copyright | Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org>
License | The Ruby License

## Description

WU-BLAST default output parser.

The parser is still incomplete and may contain many bugs, because I didn't have WU-BLAST license. It was tested under web-based WU-BLAST results and obsolete version downloaded from blast.wustl.edu/ .

## References

- blast.wustl.edu/

- www.ebi.ac.uk/blast2/

# bio/appl/iprscan/report.rb - a class for iprscan output.

Copyright | Copyright (C) 2006 Mitsuteru C. Nakao <mn@kazusa.or.jp>
License | The Ruby License

    $Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $

## Report classes for the iprscan program.

# bio/appl/sosui/report.rb - SOSUI report class

Copyright | Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
License | The Ruby License

    $Id:$

## Example

## References

- bp.nuap.nagoya-u.ac.jp/sosui/

- bp.nuap.nagoya-u.ac.jp/sosui/sosui_submit.html

# bio/appl/tcoffee.rb - T-Coffee application wrapper class

Copyright | Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

    $Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Tcoffee is a wrapper class to execute T-Coffee.

## References

- www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

- Notredame, C., Higgins, D.G. and Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217, 2000.

# bio/appl/phylip/alignment.rb - phylip multiple alignment format parser

Copyright | Copyright (C) 2006 GOTO Naohisa <ng@bioruby.org>
License | The Ruby License

    $Id: alignment.rb,v 1.2 2007/04/05 23:35:40 trevor Exp $

# About Bio::Phylip::PhylipFormat

Please refer document of Bio::Phylip::PhylipFormat class.

# bio/appl/probcons.rb - ProbCons application wrapper class

Copyright | Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

    $Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Probcons is a wrapper class to execute ProbCons (Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences).

## References

- probcons.stanford.edu/

- Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340, 2005.

# bio/appl/emboss.rb - EMBOSS wrapper

Copyright | Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org>
Copyright | Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
License | The Ruby License

$Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $

# bio/appl/targetp/report.rb - TargetP report class

Copyright | Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
License | The Ruby License

    $Id:$

## Description

TargetP class for www.cbs.dtu.dk/services/TargetP/

## Example

## References

# bio/appl/muscle.rb - MUSCLE application wrapper class

Copyright | Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

    $Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $

Bio::Muscle is a wrapper class to execute MUSCLE.

## References

- www.drive5.com/muscle/

- Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.

- Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113, 2004.

# bio/appl/meme/motif.rb - Class to represent a sequence motif

Copyright | Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,
License | The Ruby License

## Description

This file contains a minimal class to represent meme motifs

## References

- meme.sdsc.edu/meme/intro.html

TODO save on db reading from a genbank or embl object

# bio/db/fasta/defline.rb - FASTA defline parser class

Copyright | Copyright (C) 2001, 2002 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>, Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $

## Description

Bio::FastaDefline is a parser class for definition line (defline) of the FASTA format.

## Examples

    rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
    rub.entry_id       ==> 'gi|671595'
    rub.get('emb')     ==> 'CAA85678.1'
    rub.emb            ==> 'CAA85678.1'
    rub.gi             ==> '671595'
    rub.accession      ==> 'CAA85678'
    rub.accessions     ==> [ 'CAA85678' ]
    rub.acc_version    ==> 'CAA85678.1'
    rub.locus          ==> nil
    rub.list_ids       ==> [["gi", "671595"],
                            ["emb", "CAA85678.1", nil],
                            ["Perovskia abrotanoides"]]

    ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
    ckr.entry_id      ==> "gi|2495000"
    ckr.sp            ==> "CCKR_CAVPO"
    ckr.pir           ==> "I51898"
    ckr.gb            ==> "AAB29504.1"
    ckr.gi            ==> "2495000"
    ckr.accession     ==> "AAB29504"
    ckr.accessions    ==> ["Q63931", "AAB29504"]
    ckr.acc_version   ==> "AAB29504.1"
    ckr.locus         ==> nil
    ckr.description   ==>
      "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
    ckr.descriptions  ==>
      ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
       "cholecystokinin A receptor - guinea pig",
       "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
    ckr.words         ==>
      ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
       "receptor", "type"]
    ckr.id_strings    ==>
      ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
       "544724", "AAB29504.1", "Cavia"]
    ckr.list_ids      ==>
      [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
       ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
       ["gb", "AAB29504.1", nil], ["Cavia"]]

## References

- FASTA format (WikiPedia) en.wikipedia.org/wiki/FASTA_format

- Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml

require 'bio/sequence'

# bio/db/kegg/genes.rb - KEGG/GENES database class

Copyright | Copyright (C) 2001, 2002, 2006, 2010 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

## KEGG GENES parser

See www.genome.jp/kegg/genes.html

### Examples

    require 'bio/io/fetch'
    entry_string = Bio::Fetch.query('genes', 'b0002')

    entry = Bio::KEGG::GENES.new(entry_string)

    # ENTRY
    p entry.entry       # => Hash

    p entry.entry_id    # => String
    p entry.division    # => String
    p entry.organism    # => String

    # NAME
    p entry.name        # => String
    p entry.names       # => Array

    # DEFINITION
    p entry.definition  # => String
    p entry.eclinks     # => Array

    # PATHWAY
    p entry.pathway     # => String
    p entry.pathways    # => Hash

    # POSITION
    p entry.position    # => String
    p entry.chromosome  # => String
    p entry.gbposition  # => String
    p entry.locations   # => Bio::Locations

    # MOTIF
    p entry.motifs      # => Hash of Array

    # DBLINKS
    p entry.dblinks     # => Hash of Array

    # STRUCTURE
    p entry.structure   # => Array

    # CODON_USAGE
    p entry.codon_usage # => Hash
    p entry.cu_list     # => Array

    # AASEQ
    p entry.aaseq       # => Bio::Sequence::AA
    p entry.aalen       # => Fixnum

    # NTSEQ
    p entry.ntseq       # => Bio::Sequence::NA
    p entry.naseq       # => Bio::Sequence::NA
    p entry.ntlen       # => Fixnum
    p entry.nalen       # => Fixnum

# bio/db/kegg/taxonomy.rb - KEGG taxonomy parser class

Copyright | Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

    $Id:$

# bio/db/kegg/keggtab.rb - KEGG keggtab class

Copyright | Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org> Copyright (C) 2003, 2006 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

    $Id: keggtab.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $

# bio/db/kegg/common.rb - Common methods for KEGG database classes

Copyright | Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>
Copyright | Copyright (C) 2003 Masumi Itoh <m@bioruby.org>
Copyright | Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>
License | The Ruby License

## Description

Note that the modules in this file are intended to be Bio::KEGG::* internal use only.

This file contains modules that implement methods commonly used from KEGG database parser classes.

# bio/db/pdb/residue.rb - residue class for PDB

Copyright | Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# Bio::PDB::Residue

# Bio::PDB::Heterogen

# bio/db/pdb/chain.rb - chain class for PDB

Copyright | Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# Bio::PDB::Chain

Please refer Bio::PDB::Chain.

# bio/db/pdb/chemicalcomponent.rb - PDB Chemical Component Dictionary parser

Copyright | Copyright (C) 2006 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
License | The Ruby License

# About Bio::PDB::ChemicalComponent

Please refer Bio::PDB::ChemicalComponent.

# References

- ((<URL:deposit.pdb.org/cc_dict_tut.html>))

- deposit.pdb.org/het_dictionary.txt

# bio/db/pdb/model.rb - model class for PDB

Copyright | Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org>
License | The Ruby License

# Bio::PDB::Model

Please refer Bio::PDB::Model.

definition of the PDB class

Autoload definition

bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (cbri.umn.edu)
License | The Ruby License

    $Id:$

bio/db/soft.rb - Interface for SOFT formatted files

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

    $Id:$

# bio/location.rb - Locations/Location class (GenBank location format)

Copyright

Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>

    2006       Jan Aerts <jan.aerts@bbsrc.ac.uk>
    2008       Naohisa Goto <ng@bioruby.org>

License | The Ruby License

$Id:$

# bio/sequence.rb - biological sequence class

Copyright | Copyright (C) 2000-2006 Toshiaki Katayama <k@bioruby.org>, Yoshinori K. Okuji <okuji@enbug.org>, Naohisa Goto <ng@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jan.aerts@bbsrc.ac.uk>
License | The Ruby License

# bio/compat/references.rb - Obsoleted References class

Copyright | Copyright (C) 2008 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jandot@bioruby.org>, Naohisa Goto <ng@bioruby.org>
License | The Ruby License

$Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $

## Description

The Bio::References class was obsoleted after BioRuby 1.2.1. To keep compatibility, some wrapper methods are provided in this file. As the compatibility methods (and Bio::References) will soon be removed, Please change your code not to use Bio::References.

Note that Bio::Reference is different from Bio::References. Bio::Reference still exists for storing a reference information in sequence entries.

# bio/data/codontable.rb - Codon Table

Copyright | Copyright (C) 2001, 2004 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

## Data source

Data in this class is converted from the NCBI's genetic codes page.

    * ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))

### Examples

Obtain a codon table No.1 -- Standard (Eukaryote)

    table = Bio::CodonTable[1]

Obtain a copy of the codon table No.1 to modify. In this example, reassign a seleno cystein ('U') to the 'tga' codon.

    table = Bio::CodonTable.copy(1)
    table['tga'] = 'U'

Create a new codon table by your own from the Hash which contains pairs of codon and amino acid. You can also define the table name in the second argument.

    hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... }
    table = Bio::CodonTable.new(hash, "my codon table")

Obtain a translated amino acid by codon.

    table = Bio::CodonTable[1]
    table['ttt']  # => F

Reverse translation of a amino acid into a list of relevant codons.

    table = Bio::CodonTable[1]
    table.revtrans("A")  # => ["gcg", "gct", "gca", "gcc"]

# bio/data/na.rb - Nucleic Acids

Copyright | Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

## Synopsis

Bio::NucleicAcid class contains data related to nucleic acids.

## Usage

Examples:

    require 'bio'

    puts "### na = Bio::NucleicAcid.new"
    na = Bio::NucleicAcid.new

    puts "# na.to_re('yrwskmbdhvnatgc')"
    p na.to_re('yrwskmbdhvnatgc')

    puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
    p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')

    puts "# na.weight('A')"
    p na.weight('A')

    puts "# Bio::NucleicAcid.weight('A')"
    p Bio::NucleicAcid.weight('A')

    puts "# na.weight('atgc')"
    p na.weight('atgc')

    puts "# Bio::NucleicAcid.weight('atgc')"
    p Bio::NucleicAcid.weight('atgc')

# bio/data/aa.rb - Amino Acids

Copyright | Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

# bio.rb - Loading all BioRuby modules

Copyright | Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>
License | The Ruby License

$Id:$

### Constants

BIORUBY_EXTRA_VERSION

  Extra version specifier (String or nil). Existance of the value indicates pre-release version or modified version.

  nil | Release version.
  ".0000"..".4999" | Release version with patches.
  ".5000" | Development unstable version.
  ".5001"..".8999" | Pre-alpha version.
  "-alphaN" (N=0..99) | Alpha version.
  "-preN" (N=0..99) | Pre-release test version.
  "-rcN" (N=0..99) | Release candidate version.

BIORUBY_VERSION

  BioRuby version (Array containing Integer)

BIORUBY_VERSION_ID

  Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable.

### Public Class Methods

method_missing(*args) click to toggle source

Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)

    # File lib/bio.rb, line 309
    def self.method_missing(*args)
      require 'bio/shell'
      extend Bio::Shell
      public_class_method(*Bio::Shell.private_instance_methods)
      if Bio.respond_to?(args.first)
        Bio.send(*args)
      else
        raise NameError
      end
    end

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