Section 3

Section 3 of the manual describes all library functions excluding the library functions (system call wrappers) described in Section 2, which implement system calls.

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Bio::Search::GenericDatabase: Generic implementation of Bio::Search::DatabaseI
Bio::Search::GenericStatistics: An object for statistics
Bio::Search::HSP::BlastHSP: Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::BlastPullHSP: A parser and HSP object for BlastN hsps
Bio::Search::HSP::FastaHSP: HSP object for FASTA specific data
Bio::Search::HSP::GenericHSP: A "Generic" implementation of a High Scoring Pair
Bio::Search::HSP::HMMERHSP: A HSP object for HMMER results
Bio::Search::HSP::HSPFactory: A factory to create Bio::Search::HSP::HSPI objects
Bio::Search::HSP::HSPI: Interface for a High Scoring Pair in a similarity search result
Bio::Search::HSP::HmmpfamHSP: A parser and HSP object for hmmpfam hsps
Bio::Search::HSP::ModelHSP: A HSP object for model-based searches
Bio::Search::HSP::PSLHSP: A HSP for PSL output
Bio::Search::HSP::PsiBlastHSP: Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::PullHSPI: Bio::Search::HSP::HSPI interface for pull parsers
Bio::Search::HSP::WABAHSP: HSP object suitable for describing WABA alignments
Bio::Search::Hit::BlastHit: Blast-specific subclass of Bio::Search::Hit::GenericHit
Bio::Search::Hit::BlastPullHit: A parser and hit object for BLASTN hits
Bio::Search::Hit::Fasta: Hit object specific for Fasta-generated hits
Bio::Search::Hit::GenericHit: A generic implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::HMMERHit: A Hit module for HMMER hits
Bio::Search::Hit::HitFactory: A factory to create Bio::Search::Hit::HitI objects
Bio::Search::Hit::HitI: Interface for a hit in a similarity search result
Bio::Search::Hit::HmmpfamHit: A parser and hit object for hmmpfam hits
Bio::Search::Hit::ModelHit: A model-based implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::PsiBlastHit: Bioperl BLAST Hit object
Bio::Search::Hit::PullHitI: Bio::Search::Hit::HitI interface for pull parsers
Bio::Search::Hit::hmmer3Hit: DESCRIPTION of Object
Bio::Search::Iteration::GenericIteration: A generic implementation of the Bio::Search::Iteration::IterationI interface
Bio::Search::Iteration::IterationI: Abstract interface to an iteration from an iterated search result, such as PSI-BLAST
Bio::Search::Processor: DESCRIPTION of Object
Bio::Search::Result::BlastPullResult: A parser and result object for BLASTN results
Bio::Search::Result::BlastResult: Blast-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::CrossMatchResult: CrossMatch-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::GenericResult: Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results
Bio::Search::Result::HMMERResult: A Result object for HMMER results
Bio::Search::Result::HmmpfamResult: A parser and result object for hmmpfam results
Bio::Search::Result::INFERNALResult: A Result object for INFERNAL results
Bio::Search::Result::PullResultI: Bio::Search::Result::ResultI interface for 'pull' parsers
Bio::Search::Result::ResultFactory: A factory to create Bio::Search::Result::ResultI objects
Bio::Search::Result::ResultI: Abstract interface to Search Result objects
Bio::Search::Result::WABAResult: Result object for WABA alignment output
Bio::Search::Result::hmmer3Result: DESCRIPTION of Object
Bio::Search::SearchUtils: Utility functions for Bio::Search:: objects
Bio::Search::StatisticsI: A Base object for statistics
Bio::Search::Tiling::MapTileUtils: utilities for manipulating closed intervals for an HSP tiling algorithm
Bio::Search::Tiling::MapTiling: An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
Bio::Search::Tiling::TilingI: Abstract interface for an HSP tiling module
Bio::SearchIO: Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
Bio::SearchIO::EventHandlerI: An abstract Event Handler for Search Result parsing
Bio::SearchIO::FastHitEventBuilder: Event Handler for SearchIO events
Bio::SearchIO::IteratedSearchResultEventBuilder: Event Handler for SearchIO events
Bio::SearchIO::SearchResultEventBuilder: Event Handler for SearchIO events
Bio::SearchIO::SearchWriterI: Interface for outputting parsed Search results
Bio::SearchIO::Writer::GbrowseGFF: Interface for outputting parsed search results in Gbrowse GFF format
Bio::SearchIO::Writer::HSPTableWriter: Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HTMLResultWriter: write a Bio::Search::ResultI in HTML
Bio::SearchIO::Writer::HitTableWriter: Tab-delimited data for Bio::Search::Hit::HitI objects
Bio::SearchIO::Writer::ResultTableWriter: Outputs tab-delimited data for each Bio::Search::Result::ResultI object
Bio::SearchIO::Writer::TextResultWriter: Object to implement writing a Bio::Search::ResultI in Text
Bio::SearchIO::axt: a parser for axt format reports
Bio::SearchIO::blast: Event generator for event based parsing of blast reports
Bio::SearchIO::blast_pull: A parser for BLAST output
Bio::SearchIO::blasttable: Driver module for SearchIO for parsing NCBI -m 8/9 format
Bio::SearchIO::cross_match: CrossMatch-specific subclass of Bio::SearchIO
Bio::SearchIO::erpin: SearchIO-based ERPIN parser
Bio::SearchIO::exonerate: parser for Exonerate
Bio::SearchIO::fasta: A SearchIO parser for FASTA results
Bio::SearchIO::gmap_f9: Event generator for parsing gmap reports (Z format)
Bio::SearchIO::hmmer: A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
Bio::SearchIO::hmmer2: A parser for HMMER output (hmmpfam, hmmsearch)
Bio::SearchIO::hmmer3: Bio::SearchIO::hmmer3
Bio::SearchIO::hmmer_pull: A parser for HMMER output
Bio::SearchIO::infernal: SearchIO-based Infernal parser
Bio::SearchIO::megablast: a driver module for Bio::SearchIO to parse megablast reports (format 0)
Bio::SearchIO::psl: A parser for PSL output (UCSC)
Bio::SearchIO::rnamotif: SearchIO-based RNAMotif parser
Bio::SearchIO::sim4: parser for Sim4 alignments
Bio::SearchIO::waba: SearchIO parser for Jim Kent WABA program alignment output
Bio::SearchIO::wise: Parsing of wise output as alignments
Bio::Seq: Sequence object, with features
Bio::Seq::BaseSeqProcessor: Base implementation for a SequenceProcessor
Bio::Seq::EncodedSeq: subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Seq::LargeLocatableSeq: LocatableSeq object that stores sequence as files in the tempdir
Bio::Seq::LargePrimarySeq: 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: SeqI compliant object that stores sequence as files in /tmp
Bio::Seq::LargeSeqI: Interface class for sequences that cache their residues in a temporary file
Bio::Seq::Meta: Generic superclass for sequence objects with residue-based meta information
Bio::Seq::Meta::Array: array-based generic implementation of a sequence class with residue-based meta information
Bio::Seq::MetaI: Interface for sequence objects with residue-based meta information
Bio::Seq::PrimaryQual: Bioperl lightweight Quality Object
Bio::Seq::PrimedSeq: A sequence and a pair of primers matching on it
Bio::Seq::QualI: Interface definition for a Bio::Seq::Qual
Bio::Seq::Quality: Implementation of sequence with residue quality and trace values
Bio::Seq::RichSeq: Module implementing a sequence created from a rich sequence database entry
Bio::Seq::RichSeqI: interface for sequences from rich data sources, mostly databases
Bio::Seq::SeqBuilder: Configurable object builder for sequence stream parsers
Bio::Seq::SeqFactory: Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory
Bio::Seq::SeqFastaSpeedFactory: Rapid creation of Bio::Seq objects through a factory
Bio::Seq::SequenceTrace: Bioperl object packaging a sequence with its trace
Bio::Seq::SimulatedRead: Read with sequencing errors taken from a reference sequence