📦 libbio-perl-perl

B (continued)

• Bio::Search::BlastStatistics(3pm)An object for Blast statistics✨
• Bio::Search::BlastUtils(3pm)Utility functions for Bio::Search:: BLAST objects✨
• Bio::Search::DatabaseI(3pm)Interface for a database used in a sequence search✨
• Bio::Search::GenericDatabase(3pm)Generic implementation of Bio::Search::DatabaseI✨
• Bio::Search::GenericStatistics(3pm)An object for statistics✨
• Bio::Search::Hit::BlastHit(3pm)Blast-specific subclass of Bio::Search::Hit::GenericHit✨
• Bio::Search::Hit::BlastPullHit(3pm)A parser and hit object for BLASTN hits✨
• Bio::Search::Hit::Fasta(3pm)Hit object specific for Fasta-generated hits✨
• Bio::Search::Hit::GenericHit(3pm)A generic implementation of the Bio::Search::Hit::HitI interface✨
• Bio::Search::Hit::HitFactory(3pm)A factory to create Bio::Search::Hit::HitI objects✨
• Bio::Search::Hit::HitI(3pm)Interface for a hit in a similarity search result✨
• Bio::Search::Hit::ModelHit(3pm)A model-based implementation of the Bio::Search::Hit::HitI interface✨
• Bio::Search::Hit::PsiBlastHit(3pm)Bioperl BLAST Hit object✨
• Bio::Search::Hit::PullHitI(3pm)Bio::Search::Hit::HitI interface for pull parsers.✨
• Bio::Search::HSP::BlastHSP(3pm)Bioperl BLAST High-Scoring Pair object✨
• Bio::Search::HSP::BlastPullHSP(3pm)A parser and HSP object for BlastN hsps✨
• Bio::Search::HSP::FastaHSP(3pm)HSP object for FASTA specific data✨
• Bio::Search::HSP::GenericHSP(3pm)A "Generic" implementation of a High Scoring Pair✨
• Bio::Search::HSP::HSPFactory(3pm)A factory to create Bio::Search::HSP::HSPI objects✨
• Bio::Search::HSP::HSPI(3pm)Interface for a High Scoring Pair in a similarity search result✨
• Bio::Search::HSP::ModelHSP(3pm)A HSP object for model-based searches✨
• Bio::Search::HSP::PsiBlastHSP(3pm)Bioperl BLAST High-Scoring Pair object✨
• Bio::Search::HSP::PSLHSP(3pm)A HSP for PSL output✨
• Bio::Search::HSP::PullHSPI(3pm)Bio::Search::HSP::HSPI interface for pull parsers.✨
• Bio::Search::HSP::WABAHSP(3pm)HSP object suitable for describing WABA alignments✨
• Bio::Search::Iteration::GenericIteration(3pm)A generic implementation of the Bio::Search::Iteration::IterationI interface.✨
• Bio::Search::Iteration::IterationI(3pm)Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.✨
• Bio::Search::Processor(3pm)DESCRIPTION of Object✨
• Bio::Search::Result::BlastPullResult(3pm)A parser and result object for BLASTN results✨
• Bio::Search::Result::BlastResult(3pm)Blast-specific subclass of Bio::Search::Result::GenericResult✨
• Bio::Search::Result::CrossMatchResult(3pm)CrossMatch-specific subclass of Bio::Search::Result::GenericResult✨
• Bio::Search::Result::GenericResult(3pm)Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.✨
• Bio::Search::Result::INFERNALResult(3pm)A Result object for INFERNAL results✨
• Bio::Search::Result::PullResultI(3pm)Bio::Search::Result::ResultI interface for 'pull' parsers✨
• 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::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::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::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::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::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✨