section 3pm · Library functions 📚

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B (continued)

Bio::Search::Result::ResultFactory(3pm)A factory to create Bio::Search::Result::ResultI objects✨
Bio::Search::Result::ResultI(3pm)Abstract interface to Search Result objects✨
Bio::Search::Result::WABAResult(3pm)Result object for WABA alignment output✨
Bio::Search::SearchUtils(3pm)Utility functions for Bio::Search:: objects✨
Bio::Search::StatisticsI(3pm)A Base object for statistics✨
Bio::Search::Tiling::MapTileUtils(3pm)utilities for manipulating closed intervals for an HSP tiling algorithm✨
Bio::Search::Tiling::MapTiling(3pm)An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics✨
Bio::Search::Tiling::TilingI(3pm)Abstract interface for an HSP tiling module✨
Bio::SearchIO(3pm)Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)✨
Bio::SearchIO::axt(3pm)a parser for axt format reports✨
Bio::SearchIO::blast(3pm)Event generator for event based parsing of blast reports✨
Bio::SearchIO::blast_pull(3pm)A parser for BLAST output✨
Bio::SearchIO::blasttable(3pm)Driver module for SearchIO for parsing NCBI -m 8/9 format✨
Bio::SearchIO::cross_match(3pm)CrossMatch-specific subclass of Bio::SearchIO✨
Bio::SearchIO::erpin(3pm)SearchIO-based ERPIN parser✨
Bio::SearchIO::EventHandlerI(3pm)An abstract Event Handler for Search Result parsing✨
Bio::SearchIO::exonerate(3pm)parser for Exonerate✨
Bio::SearchIO::fasta(3pm)A SearchIO parser for FASTA results✨
Bio::SearchIO::FastHitEventBuilder(3pm)Event Handler for SearchIO events.✨
Bio::SearchIO::gmap_f9(3pm)Event generator for parsing gmap reports (Z format)✨
Bio::SearchIO::hmmer(3pm)A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)✨
Bio::SearchIO::hmmer2(3pm)A parser for HMMER output (hmmpfam, hmmsearch)✨
Bio::SearchIO::hmmer3(3pm)✨
Bio::SearchIO::hmmer_pull(3pm)A parser for HMMER output✨
Bio::SearchIO::infernal(3pm)SearchIO-based Infernal parser✨
Bio::SearchIO::IteratedSearchResultEventBuilder(3pm)Event Handler for SearchIO events.✨
Bio::SearchIO::megablast(3pm)a driver module for Bio::SearchIO to parse megablast reports (format 0)✨
Bio::SearchIO::psl(3pm)A parser for PSL output (UCSC)✨
Bio::SearchIO::rnamotif(3pm)SearchIO-based RNAMotif parser✨
Bio::SearchIO::SearchResultEventBuilder(3pm)Event Handler for SearchIO events.✨
Bio::SearchIO::SearchWriterI(3pm)Interface for outputting parsed Search results✨
Bio::SearchIO::sim4(3pm)parser for Sim4 alignments✨
Bio::SearchIO::waba(3pm)SearchIO parser for Jim Kent WABA program alignment output✨
Bio::SearchIO::wise(3pm)Parsing of wise output as alignments✨
Bio::SearchIO::Writer::GbrowseGFF(3pm)Interface for outputting parsed search results in Gbrowse GFF format✨
Bio::SearchIO::Writer::HitTableWriter(3pm)Tab-delimited data for Bio::Search::Hit::HitI objects✨
Bio::SearchIO::Writer::HSPTableWriter(3pm)Tab-delimited data for Bio::Search::HSP::HSPI objects✨
Bio::SearchIO::Writer::HTMLResultWriter(3pm)write a Bio::Search::ResultI in HTML✨
Bio::SearchIO::Writer::ResultTableWriter(3pm)Outputs tab-delimited data for each Bio::Search::Result::ResultI object.✨
Bio::SearchIO::Writer::TextResultWriter(3pm)Object to implement writing a Bio::Search::ResultI in Text.✨
Bio::Seq(3pm)Sequence object, with features✨
Bio::Seq::BaseSeqProcessor(3pm)Base implementation for a SequenceProcessor✨
Bio::Seq::EncodedSeq(3pm)subtype of Bio::LocatableSeq to store DNA that encodes a protein✨
Bio::Seq::LargeLocatableSeq(3pm)LocatableSeq object that stores sequence as files in the tempdir✨
Bio::Seq::LargePrimarySeq(3pm)PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root✨
Bio::Seq::LargeSeq(3pm)SeqI compliant object that stores sequence as files in /tmp✨
Bio::Seq::LargeSeqI(3pm)Interface class for sequences that cache their residues in a temporary file✨
Bio::Seq::Meta(3pm)Generic superclass for sequence objects with residue-based meta information✨
Bio::Seq::Meta::Array(3pm)array-based generic implementation of a sequence class with residue-based meta information✨
Bio::Seq::MetaI(3pm)Interface for sequence objects with residue-based meta information✨
Bio::Seq::PrimaryQual(3pm)Bioperl lightweight Quality Object✨
Bio::Seq::PrimedSeq(3pm)A sequence and a pair of primers matching on it✨
Bio::Seq::QualI(3pm)Interface definition for a Bio::Seq::Qual✨
Bio::Seq::Quality(3pm)Implementation of sequence with residue quality and trace values✨
Bio::Seq::RichSeq(3pm)Module implementing a sequence created from a rich sequence database entry✨
Bio::Seq::RichSeqI(3pm)interface for sequences from rich data sources, mostly databases✨
Bio::Seq::SeqBuilder(3pm)Configurable object builder for sequence stream parsers✨
Bio::Seq::SeqFactory(3pm)Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory✨
Bio::Seq::SeqFastaSpeedFactory(3pm)Rapid creation of Bio::Seq objects through a factory✨
Bio::Seq::SequenceTrace(3pm)Bioperl object packaging a sequence with its trace✨
Bio::Seq::SimulatedRead(3pm)Read with sequencing errors taken from a reference sequence✨
Bio::Seq::TraceI(3pm)Interface definition for a Bio::Seq::Trace✨
Bio::SeqAnalysisParserI(3pm)Sequence analysis output parser interface✨
Bio::SeqFeature::Amplicon(3pm)Amplicon feature✨
Bio::SeqFeature::Annotated(3pm)PLEASE PUT SOMETHING HERE✨
Bio::SeqFeature::AnnotationAdaptor(3pm)integrates SeqFeatureIs annotation✨
Bio::SeqFeature::Collection(3pm)A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.✨
Bio::SeqFeature::CollectionI(3pm)An interface for a collection of SeqFeatureI objects.✨
Bio::SeqFeature::Computation(3pm)Computation SeqFeature✨
Bio::SeqFeature::FeaturePair(3pm)hold pair feature information e.g. blast hits✨
Bio::SeqFeature::Gene::Exon(3pm)a feature representing an exon✨
Bio::SeqFeature::Gene::ExonI(3pm)Interface for a feature representing an exon✨
Bio::SeqFeature::Gene::GeneStructure(3pm)A feature representing an arbitrarily complex structure of a gene✨
Bio::SeqFeature::Gene::GeneStructureI(3pm)A feature representing an arbitrarily complex structure of a gene✨
Bio::SeqFeature::Gene::Intron(3pm)An intron feature✨
Bio::SeqFeature::Gene::NC_Feature(3pm)superclass for non-coding features✨
Bio::SeqFeature::Gene::Poly_A_site(3pm)poly A feature✨
Bio::SeqFeature::Gene::Promoter(3pm)Describes a promoter✨
Bio::SeqFeature::Gene::Transcript(3pm)A feature representing a transcript✨
Bio::SeqFeature::Gene::TranscriptI(3pm)Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.✨
Bio::SeqFeature::Gene::UTR(3pm)A feature representing an untranslated region that is part of a transcriptional unit✨
Bio::SeqFeature::Generic(3pm)Generic SeqFeature✨
Bio::SeqFeature::Lite(3pm)Lightweight Bio::SeqFeatureI class✨
Bio::SeqFeature::PositionProxy(3pm)handle features when truncation/revcom sequences span a feature✨
Bio::SeqFeature::Primer(3pm)Primer Generic SeqFeature✨
Bio::SeqFeature::Similarity(3pm)A sequence feature based on similarity✨
Bio::SeqFeature::SimilarityPair(3pm)Sequence feature based on the similarity of two sequences.✨
Bio::SeqFeature::SubSeq(3pm)Feature representing a subsequence✨
Bio::SeqFeature::Tools::FeatureNamer(3pm)generates unique persistent names for features✨
Bio::SeqFeature::Tools::IDHandler(3pm)maps $seq_feature->primary_tag✨
Bio::SeqFeature::Tools::TypeMapper(3pm)maps $seq_feature->primary_tag✨
Bio::SeqFeature::Tools::Unflattener(3pm)turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy✨
Bio::SeqFeature::TypedSeqFeatureI(3pm)a strongly typed SeqFeature✨
Bio::SeqFeatureI(3pm)Abstract interface of a Sequence Feature✨
Bio::SeqI(3pm)[Developers] Abstract Interface of Sequence (with features)✨
Bio::SeqIO(3pm)Handler for SeqIO Formats✨
Bio::SeqIO::ace(3pm)ace sequence input/output stream✨
Bio::SeqIO::asciitree(3pm)asciitree sequence input/output stream✨
Bio::SeqIO::bsml(3pm)BSML sequence input/output stream✨
Bio::SeqIO::bsml_sax(3pm)BSML sequence input/output stream using SAX✨
Bio::SeqIO::embl(3pm)EMBL sequence input/output stream✨
Bio::SeqIO::embldriver(3pm)EMBL sequence input/output stream✨
Bio::SeqIO::entrezgene(3pm)Entrez Gene ASN1 parser✨
Bio::SeqIO::fasta(3pm)fasta sequence input/output stream✨
Bio::SeqIO::fastq(3pm)fastq sequence input/output stream✨
Bio::SeqIO::FTHelper(3pm)Helper class for EMBL/Genbank feature tables✨
Bio::SeqIO::game(3pm)a class for parsing and writing game-XML✨
Bio::SeqIO::game::featHandler(3pm)a class for handling feature elements✨
Bio::SeqIO::game::gameHandler(3pm)PerlSAX handler for game-XML✨
Bio::SeqIO::game::gameSubs(3pm)a base class for game-XML parsing✨
Bio::SeqIO::game::gameWriter(3pm)a class for writing game-XML✨
Bio::SeqIO::game::seqHandler(3pm)a class for handling game-XML sequences✨
Bio::SeqIO::gbdriver(3pm)GenBank handler-based push parser✨
Bio::SeqIO::gbxml(3pm)GenBank sequence input/output stream using SAX✨
Bio::SeqIO::gcg(3pm)GCG sequence input/output stream✨
Bio::SeqIO::genbank(3pm)GenBank sequence input/output stream✨
Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data✨
Bio::SeqIO::kegg(3pm)KEGG sequence input/output stream✨
Bio::SeqIO::largefasta(3pm)method i/o on very large fasta sequence files✨
Bio::SeqIO::locuslink(3pm)LocusLink input/output stream✨
Bio::SeqIO::mbsout(3pm)input stream for output by Teshima et al.'s mbs.✨
Bio::SeqIO::metafasta(3pm)metafasta sequence input/output stream✨
Bio::SeqIO::msout(3pm)input stream for output by Hudson's ms✨
Bio::SeqIO::MultiFile(3pm)Treating a set of files as a single input stream✨
Bio::SeqIO::phd(3pm)phd file input/output stream✨
Bio::SeqIO::pir(3pm)PIR sequence input/output stream✨
Bio::SeqIO::qual(3pm).qual file input/output stream✨
Bio::SeqIO::raw(3pm)raw sequence file input/output stream✨
Bio::SeqIO::scf(3pm).scf file input/output stream✨
Bio::SeqIO::seqxml(3pm)SeqXML sequence input/output stream✨
Bio::SeqIO::swiss(3pm)Swissprot sequence input/output stream✨
Bio::SeqIO::swissdriver(3pm)SwissProt/UniProt handler-based push parser✨
Bio::SeqIO::tab(3pm)nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"✨
Bio::SeqIO::table(3pm)sequence input/output stream from a delimited table✨
Bio::SeqIO::tigr(3pm)TIGR XML sequence input/output stream✨
Bio::SeqIO::tigrxml(3pm)Parse TIGR (new) XML✨
Bio::SeqIO::tinyseq(3pm)reading/writing sequences in NCBI TinySeq format✨
Bio::SeqIO::tinyseq::tinyseqHandler(3pm)XML event handlers to support NCBI TinySeq XML parsing✨
Bio::SeqUtils(3pm)Additional methods for PrimarySeq objects✨
Bio::SimpleAlign(3pm)Multiple alignments held as a set of sequences✨
Bio::SimpleAnalysisI(3pm)A simple interface to any (local or remote) analysis tool✨
Bio::Species(3pm)Generic species object.✨
Bio::Taxon(3pm)A node in a represented taxonomy✨
Bio::Tools::Alignment::Consed(3pm)A module to work with objects from consed .ace files✨
Bio::Tools::Alignment::Trim(3pm)A kludge to do specialized trimming of sequence based on quality.✨
Bio::Tools::AmpliconSearch(3pm)Find amplicons in a template using degenerate PCR primers✨
Bio::Tools::Analysis::SimpleAnalysisBase(3pm)abstract superclass for SimpleAnalysis implementations✨
Bio::Tools::AnalysisResult(3pm)Base class for analysis result objects and parsers✨
Bio::Tools::Blat(3pm)parser for Blat program✨
Bio::Tools::CodonTable(3pm)Codon table object✨
Bio::Tools::Coil(3pm)parser for Coil output✨
Bio::Tools::ECnumber(3pm)representation of EC numbers (Enzyme Classification)✨
Bio::Tools::EMBOSS::Palindrome(3pm)parse EMBOSS palindrome output✨
Bio::Tools::EPCR(3pm)Parse ePCR output and make features✨
Bio::Tools::Eponine(3pm)Results of one Eponine run✨
Bio::Tools::Est2Genome(3pm)Parse est2genome output, makes simple Bio::SeqFeature::Generic objects✨
Bio::Tools::ESTScan(3pm)Results of one ESTScan run✨
Bio::Tools::EUtilities(3pm)NCBI eutil XML parsers.✨
Bio::Tools::EUtilities::EUtilDataI(3pm)EUtil data object interface.✨
Bio::Tools::EUtilities::EUtilParameters(3pm)Manipulation of NCBI eutil-based parameters for remote database requests.✨
Bio::Tools::EUtilities::History(3pm)Lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).✨
Bio::Tools::EUtilities::HistoryI(3pm)Simple extension of EUtilDataI interface class for classes which hold NCBI server history data.✨
Bio::Tools::EUtilities::Info(3pm)Interface class for storing einfo data.✨
Bio::Tools::EUtilities::Info::FieldInfo(3pm)Class for storing einfo field data.✨
Bio::Tools::EUtilities::Info::LinkInfo(3pm)Class for storing einfo link data.✨
Bio::Tools::EUtilities::Link(3pm)General API for accessing data retrieved from elink queries.✨
Bio::Tools::EUtilities::Link::LinkSet(3pm)Class for EUtils LinkSets.✨
Bio::Tools::EUtilities::Link::UrlLink(3pm)Class for EUtils UrlLinks.✨
Bio::Tools::EUtilities::Query(3pm)Parse and collect esearch, epost, espell, egquery information.✨
Bio::Tools::EUtilities::Query::GlobalQuery(3pm)Container class for egquery data.✨
Bio::Tools::EUtilities::Summary(3pm)Class for handling data output (XML) from esummary.✨
Bio::Tools::EUtilities::Summary::DocSum(3pm)Data object for document summary data from esummary.✨
Bio::Tools::EUtilities::Summary::Item(3pm)Simple layered object for DocSum item data.✨
Bio::Tools::EUtilities::Summary::ItemContainerI(3pm)Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).✨
Bio::Tools::Fgenesh(3pm)parse results of one Fgenesh run✨
Bio::Tools::FootPrinter(3pm)write sequence features in FootPrinter format✨
Bio::Tools::Geneid(3pm)Results of one geneid run✨
Bio::Tools::Genemark(3pm)Results of one Genemark run✨
Bio::Tools::Genewise(3pm)Results of one Genewise run✨
Bio::Tools::Genomewise(3pm)Results of one Genomewise run✨
Bio::Tools::Genscan(3pm)Results of one Genscan run✨
Bio::Tools::GFF(3pm)A Bio::SeqAnalysisParserI compliant GFF format parser✨
Bio::Tools::Glimmer(3pm)parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions✨
Bio::Tools::Grail(3pm)Results of one Grail run✨
Bio::Tools::GuessSeqFormat(3pm)Module for determining the sequence format of the contents of a file, a string, or through a filehandle.✨
Bio::Tools::HMMER::Domain(3pm)One particular domain hit from HMMER✨
Bio::Tools::HMMER::Results(3pm)Object representing HMMER output results✨
Bio::Tools::HMMER::Set(3pm)Set of identical domains from HMMER matches✨
Bio::Tools::Hmmpfam(3pm)Parser for Hmmpfam program✨
Bio::Tools::ipcress(3pm)Parse ipcress output and make features✨
Bio::Tools::isPcr(3pm)Parse isPcr output and make features✨
Bio::Tools::IUPAC(3pm)Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence✨
Bio::Tools::Lucy(3pm)Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR✨
Bio::Tools::Match(3pm)Parses output from Transfac's match(TM)✨
Bio::Tools::Motif(3pm)Perl implementation of the Motif protein subcellular localization method.✨
Bio::Tools::Motif::Match(3pm)Represents a match as reported by the Bio::Tools::Motif module.✨
Bio::Tools::Motif::Pattern(3pm)Represents a pattern used by the Bio::Tools::Motif module.✨
Bio::Tools::MZEF(3pm)Results of one MZEF run✨
Bio::Tools::OddCodes(3pm)Object holding alternative alphabet coding for one protein sequence✨
Bio::Tools::Phylo::Gerp(3pm)Parses output from GERP✨