section 3pm · Library functions 📚

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B (continued)

Bio::AlignIO::mase(3pm)mase sequence input/output stream✨
Bio::AlignIO::mega(3pm)Parse and Create MEGA format data files✨
Bio::AlignIO::meme(3pm)meme sequence input/output stream✨
Bio::AlignIO::metafasta(3pm)Metafasta MSA Sequence input/output stream✨
Bio::AlignIO::msf(3pm)msf sequence input/output stream✨
Bio::AlignIO::nexus(3pm)NEXUS format sequence input/output stream✨
Bio::AlignIO::pfam(3pm)pfam sequence input/output stream✨
Bio::AlignIO::phylip(3pm)PHYLIP format sequence input/output stream✨
Bio::AlignIO::po(3pm)po MSA Sequence input/output stream✨
Bio::AlignIO::proda(3pm)proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)✨
Bio::AlignIO::prodom(3pm)prodom sequence input/output stream✨
Bio::AlignIO::psi(3pm)Read/Write PSI-BLAST profile alignment files✨
Bio::AlignIO::selex(3pm)selex sequence input/output stream✨
Bio::AlignIO::stockholm(3pm)stockholm sequence input/output stream✨
Bio::AlignIO::xmfa(3pm)XMFA MSA Sequence input/output stream✨
Bio::AnalysisI(3pm)An interface to any (local or remote) analysis tool✨
Bio::AnalysisParserI(3pm)Generic analysis output parser interface✨
Bio::AnalysisResultI(3pm)Interface for analysis result objects✨
Bio::AnnotatableI(3pm)the base interface an annotatable object must implement✨
Bio::Annotation::AnnotationFactory(3pm)Instantiates a new Bio::AnnotationI (or derived class) through a factory✨
Bio::Annotation::Collection(3pm)Default Perl implementation of AnnotationCollectionI✨
Bio::Annotation::Comment(3pm)A comment object, holding text✨
Bio::Annotation::DBLink(3pm)untyped links between databases✨
Bio::Annotation::OntologyTerm(3pm)An ontology term adapted to AnnotationI✨
Bio::Annotation::Reference(3pm)Specialised DBLink object for Literature References✨
Bio::Annotation::Relation(3pm)Relationship (pairwise) with other objects SeqI and NodeI;✨
Bio::Annotation::SimpleValue(3pm)A simple scalar✨
Bio::Annotation::StructuredValue(3pm)A scalar with embedded structured information✨
Bio::Annotation::TagTree(3pm)AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.✨
Bio::Annotation::Target(3pm)Provides an object which represents a target (ie, a similarity hit) from one object to something in another database✨
Bio::Annotation::Tree(3pm)Provide a tree as an annotation to a Bio::AnnotatableI object✨
Bio::Annotation::TypeManager(3pm)Manages types for annotation collections✨
Bio::AnnotationCollectionI(3pm)Interface for annotation collections✨
Bio::AnnotationI(3pm)Annotation interface✨
Bio::ASN1::EntrezGene(3pm)Regular expression-based Perl Parser for NCBI Entrez Gene.✨
Bio::ASN1::EntrezGene::Indexer(3pm)Indexes NCBI Sequence files.✨
Bio::ASN1::Sequence(3pm)Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.✨
Bio::ASN1::Sequence::Indexer(3pm)Indexes NCBI Sequence files.✨
Bio::Biblio(3pm)a bibliographic query service module✨
Bio::Biblio::Article(3pm)representation of a general article✨
Bio::Biblio::BiblioBase(3pm)an abstract base for other biblio classes✨
Bio::Biblio::Book(3pm)Representation of a book✨
Bio::Biblio::BookArticle(3pm)representation of a book article✨
Bio::Biblio::IO(3pm)Handling the bibliographic references✨
Bio::Biblio::IO::medline2ref(3pm)a converter of a raw hash to MEDLINE citations✨
Bio::Biblio::IO::medlinexml(3pm)a converter of XML files with MEDLINE citations✨
Bio::Biblio::IO::pubmed2ref(3pm)a converter of a raw hash to PUBMED citations✨
Bio::Biblio::IO::pubmedxml(3pm)a converter of XML files with PUBMED citations✨
Bio::Biblio::Journal(3pm)representation of a journal✨
Bio::Biblio::JournalArticle(3pm)representation of a journal article✨
Bio::Biblio::MedlineArticle(3pm)representation of a MEDLINE article✨
Bio::Biblio::MedlineBook(3pm)representation of a MEDLINE book✨
Bio::Biblio::MedlineBookArticle(3pm)representation of a MEDLINE book article✨
Bio::Biblio::MedlineJournal(3pm)representation of a MEDLINE journal✨
Bio::Biblio::MedlineJournalArticle(3pm)representation of a MEDLINE journal article✨
Bio::Biblio::Organisation(3pm)representation of an organisation✨
Bio::Biblio::Patent(3pm)representation of a patent✨
Bio::Biblio::Person(3pm)representation of a person✨
Bio::Biblio::Proceeding(3pm)representation of a conference proceeding✨
Bio::Biblio::Provider(3pm)representation of a general provider✨
Bio::Biblio::PubmedArticle(3pm)representation of a PUBMED article✨
Bio::Biblio::PubmedBookArticle(3pm)representation of a PUBMED book article✨
Bio::Biblio::PubmedJournalArticle(3pm)representation of a PUBMED journal article✨
Bio::Biblio::Ref(3pm)representation of a bibliographic reference✨
Bio::Biblio::Service(3pm)representation of a provider of type service✨
Bio::Biblio::TechReport(3pm)representation of a technical report✨
Bio::Biblio::Thesis(3pm)representation of thesis✨
Bio::Biblio::WebResource(3pm)representation of a web resource✨
Bio::Chado::NaturalDiversity::Reports(3pm)Collection of functions for formatting Chado stock related data✨
Bio::Chado::Schema(3pm)A standard DBIx::Class layer for the Chado database schema.✨
Bio::Chado::Schema::Test(3pm)Library to be used by Bio::Chado::Schema test scripts.✨
Bio::Chado::Schema::Util(3pm)utility functions shared by Bio::Chado::Schema objects✨
Bio::Cluster(3pm)BioPerl cluster modules✨
Bio::Cluster::ClusterFactory(3pm)Instantiates a new Bio::ClusterI (or derived class) through a factory✨
Bio::Cluster::FamilyI(3pm)Family Interface✨
Bio::Cluster::SequenceFamily(3pm)Sequence Family object✨
Bio::Cluster::UniGene(3pm)UniGene object✨
Bio::Cluster::UniGeneI(3pm)abstract interface of UniGene object✨
Bio::ClusterI(3pm)Cluster Interface✨
Bio::ClusterIO(3pm)Handler for Cluster Formats✨
Bio::ClusterIO::dbsnp(3pm)dbSNP input stream✨
Bio::ClusterIO::unigene(3pm)UniGene input stream✨
Bio::CodonUsage::IO(3pm)for reading and writing codon usage tables to file✨
Bio::CodonUsage::Table(3pm)for access to the Codon usage Database at http://www.kazusa.or.jp/codon.✨
Bio::Coordinate(3pm)Modules for working with biological coordinates✨
Bio::Coordinate::Chain(3pm)Mapping locations through a chain of coordinate mappers.✨
Bio::Coordinate::Collection(3pm)Noncontinuous match between two coordinate sets.✨
Bio::Coordinate::ExtrapolatingPair(3pm)Continuous match between two coordinate sets.✨
Bio::Coordinate::GeneMapper(3pm)Transformations between gene related coordinate systems.✨
Bio::Coordinate::Graph(3pm)Finds shortest path between nodes in a graph.✨
Bio::Coordinate::MapperI(3pm)Interface describing coordinate mappers.✨
Bio::Coordinate::Pair(3pm)Continuous match between two coordinate sets.✨
Bio::Coordinate::Result(3pm)Results from coordinate transformation.✨
Bio::Coordinate::Result::Gap(3pm)Another name for Bio::Location::Simple.✨
Bio::Coordinate::Result::Match(3pm)Another name for Bio::Location::Simple.✨
Bio::Coordinate::ResultI(3pm)Interface to identify coordinate mapper results.✨
Bio::Coordinate::Utils(3pm)Additional methods to create Bio::Coordinate objects.✨
Bio::Das::FeatureTypeI(3pm)Simple interface to Sequence Ontology feature types✨
Bio::Das::Lite(3pm)Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)✨
Bio::Das::SegmentI(3pm)DAS-style access to a feature database✨
Bio::DasI(3pm)DAS-style access to a feature database✨
Bio::DB::Ace(3pm)Database object interface to ACeDB servers✨
Bio::DB::Bam::Alignment(3pm)The SAM/BAM alignment object✨
Bio::DB::Bam::AlignWrapper(3pm)Add high-level methods to Bio::DB::Bam::Alignment✨
Bio::DB::Bam::Pileup(3pm)Object passed to pileup() callback✨
Bio::DB::Bam::PileupWrapper(3pm)Add high-level methods to Bio::DB::Bam::Pileup✨
Bio::DB::Bam::Query(3pm)Object representing the query portion of a BAM/SAM alignment✨
Bio::DB::Bam::Target(3pm)Object representing the query portion of a BAM/SAM alignment in NATIVE alignment✨
Bio::DB::Biblio::biofetch(3pm)a BioFetch-based access to a bibliographic citation retrieval✨
Bio::DB::Biblio::eutils(3pm)access to PubMed's bibliographic query service✨
Bio::DB::Biblio::soap(3pm)a SOAP-based access to a bibliographic query service✨
Bio::DB::BiblioI(3pm)an interface to a Bibliographic Query Service✨
Bio::DB::BioFetch(3pm)Database object interface to BioFetch retrieval✨
Bio::DB::DBFetch(3pm)Database object for retrieving using the dbfetch script✨
Bio::DB::EMBL(3pm)Database object interface for EMBL entry retrieval✨
Bio::DB::EntrezGene(3pm)Database object interface to Entrez Gene✨
Bio::DB::ESoap(3pm)Client for the NCBI Entrez EUtilities SOAP server✨
Bio::DB::ESoap::WSDL(3pm)WSDL parsing for Entrez SOAP EUtilities✨
Bio::DB::EUtilities(3pm)Webagent which interacts with and retrieves data from NCBI's eUtils.✨
Bio::DB::Failover(3pm)A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs✨
Bio::DB::Fasta(3pm)Fast indexed access to fasta files✨
Bio::DB::FileCache(3pm)In file cache for BioSeq objects✨
Bio::DB::Flat(3pm)Interface for indexed flat files✨
Bio::DB::Flat::BDB(3pm)Interface for BioHackathon standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::embl(3pm)embl adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::fasta(3pm)fasta adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::genbank(3pm)genbank adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::swiss(3pm)swissprot adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BinarySearch(3pm)BinarySearch search indexing system for sequence files✨
Bio::DB::GenBank(3pm)Database object interface to GenBank✨
Bio::DB::GenericWebAgent(3pm)helper base class for parameter-based remote server access and response retrieval.✨
Bio::DB::GenPept(3pm)Database object interface to GenPept✨
Bio::DB::GFF(3pm)Storage and retrieval of sequence annotation data✨
Bio::DB::GFF::Adaptor::ace(3pm)ace interface (for multiple inheritance)✨
Bio::DB::GFF::Adaptor::berkeleydb(3pm)Bio::DB::GFF database adaptor for in-memory databases✨
Bio::DB::GFF::Adaptor::berkeleydb::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::berkeleydb✨
Bio::DB::GFF::Adaptor::biofetch(3pm)Cache BioFetch objects in a Bio::DB::GFF database✨
Bio::DB::GFF::Adaptor::biofetch_oracle(3pm)Cache BioFetch objects in a Bio::DB::GFF database✨
Bio::DB::GFF::Adaptor::dbi(3pm)Database adaptor for DBI (SQL) databases✨
Bio::DB::GFF::Adaptor::dbi::caching_handle(3pm)Cache for database handles✨
Bio::DB::GFF::Adaptor::dbi::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::dbi✨
Bio::DB::GFF::Adaptor::dbi::mysql(3pm)Database adaptor for a specific mysql schema✨
Bio::DB::GFF::Adaptor::dbi::mysqlace(3pm)Unholy union between mysql GFF database and acedb database✨
Bio::DB::GFF::Adaptor::dbi::mysqlcmap(3pm)Database adaptor for an integraded CMap/GBrowse mysql schema✨
Bio::DB::GFF::Adaptor::dbi::mysqlopt(3pm)Deprecated database adaptor✨
Bio::DB::GFF::Adaptor::dbi::oracle(3pm)Database adaptor for a specific oracle schema✨
Bio::DB::GFF::Adaptor::dbi::oracleace(3pm)Unholy union between oracle GFF database and acedb database✨
Bio::DB::GFF::Adaptor::dbi::pg(3pm)Database adaptor for a specific postgres schema✨
Bio::DB::GFF::Adaptor::dbi::pg_fts(3pm)Database adaptor for a specific postgres schema with a TSearch2 implementation✨
Bio::DB::GFF::Adaptor::memory(3pm)Bio::DB::GFF database adaptor for in-memory databases✨
Bio::DB::GFF::Adaptor::memory::feature_serializer(3pm)utility methods for serializing and deserializing GFF features✨
Bio::DB::GFF::Adaptor::memory::iterator(3pm)iterator for Bio::DB::GFF::Adaptor::memory✨
Bio::DB::GFF::Aggregator(3pm)Aggregate GFF groups into composite features✨
Bio::DB::GFF::Aggregator::alignment(3pm)Alignment aggregator✨
Bio::DB::GFF::Aggregator::clone(3pm)Clone aggregator✨
Bio::DB::GFF::Aggregator::coding(3pm)The Coding Region Aggregator✨
Bio::DB::GFF::Aggregator::gene(3pm)Sequence Ontology Geene✨
Bio::DB::GFF::Aggregator::match(3pm)Match aggregator✨
Bio::DB::GFF::Aggregator::match_gap(3pm)GFF3 match aggregator✨
Bio::DB::GFF::Aggregator::none(3pm)No aggregation✨
Bio::DB::GFF::Aggregator::orf(3pm)An aggregator for orf regions✨
Bio::DB::GFF::Aggregator::processed_transcript(3pm)Sequence Ontology Transcript✨
Bio::DB::GFF::Aggregator::reftranscript(3pm)Aggregates references transcripts✨
Bio::DB::GFF::Aggregator::so_transcript(3pm)Sequence Ontology Transcript✨
Bio::DB::GFF::Aggregator::transcript(3pm)Transcript aggregator✨
Bio::DB::GFF::Aggregator::ucsc_acembly(3pm)UCSC acembly aggregator✨
Bio::DB::GFF::Aggregator::ucsc_ensgene(3pm)UCSC ensGene aggregator✨
Bio::DB::GFF::Aggregator::ucsc_genscan(3pm)UCSC genscan aggregator✨
Bio::DB::GFF::Aggregator::ucsc_refgene(3pm)UCSC refGene aggregator✨
Bio::DB::GFF::Aggregator::ucsc_sanger22(3pm)UCSC sanger22 aggregator✨
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo(3pm)UCSC sanger22pseudo aggregator✨
Bio::DB::GFF::Aggregator::ucsc_softberry(3pm)UCSC softberry aggregator✨
Bio::DB::GFF::Aggregator::ucsc_twinscan(3pm)UCSC twinscan aggregator✨
Bio::DB::GFF::Aggregator::ucsc_unigene(3pm)UCSC UniGene aggregator✨
Bio::DB::GFF::Aggregator::waba_alignment(3pm)A WABA alignment✨
Bio::DB::GFF::Aggregator::wormbase_gene(3pm)Wormbase gene aggregator✨
Bio::DB::GFF::Featname(3pm)The name of a feature✨
Bio::DB::GFF::Feature(3pm)A relative segment identified by a feature type✨
Bio::DB::GFF::Homol(3pm)A segment of DNA that is homologous to another✨
Bio::DB::GFF::RelSegment(3pm)Sequence segment with relative coordinate support✨
Bio::DB::GFF::Segment(3pm)Simple DNA segment object✨
Bio::DB::GFF::Typename(3pm)The name of a feature type✨
Bio::DB::GFF::Util::Binning(3pm)binning utility for Bio::DB::GFF index✨
Bio::DB::GFF::Util::Rearrange(3pm)rearrange utility✨
Bio::DB::HTS(3pm)Read files using HTSlib including BAM/CRAM, Tabix and BCF database files✨
Bio::DB::HTS::Alignment(3pm)The HTS alignment object✨
Bio::DB::HTS::AlignWrapper(3pm)Add high-level methods to Bio::DB::HTS::Alignment✨
Bio::DB::HTS::ConfigData(3pm)Configuration for Bio::DB::HTS✨
Bio::DB::HTS::Constants(3pm)Constants for use with SAM/BAM✨
Bio::DB::HTS::Faidx(3pm)Perl extension for accessing bgzip compressed and indexed FASTA using htslib✨
Bio::DB::HTS::FetchIterator(3pm)✨
Bio::DB::HTS::Kseq(3pm)Bindings to Kseq✨
Bio::DB::HTS::Kseq::Iterator(3pm)The Kseq iterator✨
Bio::DB::HTS::Kseq::Record(3pm)Entry from a Kseq iterator✨
Bio::DB::HTS::Pileup(3pm)Object passed to pileup() callback✨
Bio::DB::HTS::PileupWrapper(3pm)Add high-level methods to Bio::DB::HTS::Pileup✨
Bio::DB::HTS::Query(3pm)Object representing the query portion of a BAM/SAM alignment✨
Bio::DB::HTS::ReadIterator(3pm)✨
Bio::DB::HTS::Segment(3pm)✨
Bio::DB::HTS::Tabix(3pm)Object oriented access to the underlying tbx C methods✨