892 results (0.23 seconds)
++ed by:
CJFIELDS FIBO GENEHACK MAJENSEN THALJEF

5 PAUSE user(s)
6 non-PAUSE user(s).

Christopher Fields
Documentation
Bio::LocatableSeq - A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
Bio::Tools::Run::WrapperBase::CommandExts - Extensions to WrapperBase for handling programs with commands *ALPHA*
BioPerl - Perl Modules for Biology
Deobfuscator - get BioPerl method and package information from a Berkeley DB
authors.pl - check modules and scripts for authors not in AUTHORS file
bp_aacomp - amino acid composition of protein sequences
bp_biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank
bp_bioflat_index.pl - index sequence files using Bio::DB::Flat
bp_biogetseq - sequence retrieval using OBDA registry
bp_bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
bp_chaos_plot - a chaos plot from DNA and RNA sequences
bp_classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
bp_dbsplit - script to split an input set of database(s) into smaller pieces
bp_download_query_genbank - script to query Genbank and retrieve records
bp_extract_feature_seq - extract the corresponding sequence for a specified feature type
bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
bp_fetch.pl - fetches sequences from bioperl indexed databases
bp_filter_search - filters searchio results, outputting a tab delimited summary
bp_flanks - finding flanking sequences for a variant in a sequence position
bp_gccalc - GC content of nucleotide sequences
bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
bp_generate_histogram.pl - Generate a histogram of Bio::DB::GFF features
bp_heterogeneity_test - a test for distinguishing between selection and population expansion.
bp_hivq.PL - an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery
bp_hmmer_to_table - turn HMMER output into tabular format
bp_index.pl - indexes files for use by bp_fetch.pl
bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
bp_make_mrna_protein - Convert an input mRNA/cDNA sequence into protein
bp_mask_by_search - mask sequence(s) based on its alignment results
bp_meta_gff.pl - Get/set Bio::DB::GFF meta-data
bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates
bp_mutate.pl - randomly mutagenize a single protein or DNA sequence
bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
bp_oligo_count - oligo count and frequency
bp_pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences
bp_parse_hmmsearch - parse single/multiple HMMSEARCH results file(s) with different output options
bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
bp_query_entrez_taxa - query Entrez taxonomy database and print out information
bp_remote_blast.pl - script for submitting jobs to a remote blast server (ncbi blast queue at this time)
bp_revtrans-motif - Reverse translate a Profam-like protein motif
bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
bp_search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
bp_seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
bp_seqconvert - generic BioPerl sequence format converter
bp_seqfeature_load.pl - Load GFF into a SeqFeature database
bp_seqpart.pl - Takes one or more sequence files and splits them into a number of load balanced files.
bp_seqret - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
bp_seqretsplit - split a sequence (or stream) into a single file per sequence
bp_split_seq - splits a sequence into equal sized chunks with an optional overlapping range
bp_taxid4species - simple script which returns the NCBI Taxonomic id for a requested species
bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
bp_translate_seq - translates a sequence
bp_tree2pag - convert Bio::TreeIO parseable format trees to pagel format
bp_unflatten_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
bpsreformat - convert sequence formats
check_NAMEs.pl - check NAME in module POD has fully qualified object name
check_URLs.pl - validate URLs located in module code and POD
cvs2cl_by_file.pl - convert cvs log messages to changelogs
deob_index.pl - extracts BioPerl documentation and indexes it in a database for easy retrieval
dependencies.pl - check modules and scripts for dependencies not in core
deprecated.pl - Check modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.
fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
find_mod_deps.pl - inspect only hard-coded dependencies of sets of perl files
modules.pl - information about modules in BioPerl core
pod.pl - check the POD documentation syntax in modules and scripts
search2bsml - Turn SearchIO parseable reports(s) into a BSML report
symlink_script.pl - install script to create symbolic links
tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
Modules
Bio::Align::AlignI - An interface for describing sequence alignments.
Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects
Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)
Bio::Align::StatisticsI - Calculate some statistics for an alignment
Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects
Bio::AlignIO - Handler for AlignIO Formats
Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data
Bio::AlignIO::arp - ARP MSA Sequence input/output stream
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
Bio::AlignIO::clustalw - clustalw sequence input/output stream
Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream
Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
Bio::AlignIO::mase - mase sequence input/output stream
Bio::AlignIO::mega - Parse and Create MEGA format data files
Bio::AlignIO::meme - meme sequence input/output stream
Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream
Bio::AlignIO::msf - msf sequence input/output stream
Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
Bio::AlignIO::pfam - pfam sequence input/output stream
Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
Bio::AlignIO::po - po MSA Sequence input/output stream
Bio::AlignIO::proda - proda sequence input/output stream
Bio::AlignIO::prodom - prodom sequence input/output stream
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
Bio::AlignIO::selex - selex sequence input/output stream
Bio::AlignIO::stockholm - stockholm sequence input/output stream
Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
Bio::AnalysisI - An interface to any (local or remote) analysis tool
Bio::AnalysisParserI - Generic analysis output parser interface
Bio::AnalysisResultI - Interface for analysis result objects
Bio::AnnotatableI - the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory
Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment - A comment object, holding text
Bio::Annotation::DBLink - untyped links between databases
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Bio::Annotation::Reference - Specialised DBLink object for Literature References
Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;
Bio::Annotation::SimpleValue - A simple scalar
Bio::Annotation::StructuredValue - A scalar with embedded structured information
Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object
Bio::Annotation::TypeManager - Manages types for annotation collections
Bio::AnnotationCollectionI - Interface for annotation collections
Bio::AnnotationI - Annotation interface
Bio::Assembly::Contig - Perl module to hold and manipulate sequence assembly contigs.
Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs.
Bio::Assembly::IO - Handler for Assembly::IO Formats
Bio::Assembly::IO::ace - module to load ACE files from various assembly programs
Bio::Assembly::IO::bowtie - An IO module for assemblies in Bowtie format *BETA*
Bio::Assembly::IO::maq - Driver to read assembly files in maq format *BETA*
Bio::Assembly::IO::phrap - driver to load phrap.out files.
Bio::Assembly::IO::sam - An IO module for assemblies in Sam format *BETA*
Bio::Assembly::IO::tigr - Driver to read and write assembly files in the TIGR Assembler v2 default format.
Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data.
Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
Bio::Assembly::Singlet - Perl module to hold and manipulate singlets from sequence assembly contigs.
Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra
Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory
Bio::Cluster::FamilyI - Family Interface
Bio::Cluster::SequenceFamily - Sequence Family object
Bio::Cluster::UniGene - UniGene object
Bio::Cluster::UniGeneI - abstract interface of UniGene object
Bio::ClusterI - Cluster Interface
Bio::ClusterIO - Handler for Cluster Formats
Bio::ClusterIO::dbsnp - dbSNP input stream
Bio::ClusterIO::unigene - UniGene input stream
Bio::CodonUsage::IO - for reading and writing codon usage tables to file
Bio::CodonUsage::Table - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::DB::Ace - Database object interface to ACeDB servers
Bio::DB::BioFetch - Database object interface to BioFetch retrieval
Bio::DB::CUTG - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
Bio::DB::EMBL - Database object interface for EMBL entry retrieval
Bio::DB::EntrezGene - Database object interface to Entrez Gene
Bio::DB::Expression - DESCRIPTION of Object
Bio::DB::Expression::geo - *** DESCRIPTION of Class
Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
Bio::DB::Fasta - Fast indexed access to fasta files
Bio::DB::FileCache - In file cache for BioSeq objects
Bio::DB::Flat - Interface for indexed flat files
Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file
Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::swiss - swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files
Bio::DB::GFF - Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance)
Bio::DB::GFF::Adaptor::berkeleydb - Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::berkeleydb::iterator - iterator for Bio::DB::GFF::Adaptor::berkeleydb
Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases
Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles
Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi
Bio::DB::GFF::Adaptor::dbi::mysql - Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::mysqlcmap - Database adaptor for an integraded CMap/GBrowse mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlopt - Deprecated database adaptor
Bio::DB::GFF::Adaptor::dbi::oracle - Database adaptor for a specific oracle schema
Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema
Bio::DB::GFF::Adaptor::dbi::pg_fts - Database adaptor for a specific postgres schema with a TSearch2 implementation
Bio::DB::GFF::Adaptor::memory - Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::memory::feature_serializer - utility methods for serializing and deserializing GFF features
Bio::DB::GFF::Adaptor::memory::iterator - iterator for Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF::Aggregator - Aggregate GFF groups into composite features
Bio::DB::GFF::Aggregator::alignment - Alignment aggregator
Bio::DB::GFF::Aggregator::clone - Clone aggregator
Bio::DB::GFF::Aggregator::coding - The Coding Region Aggregator
Bio::DB::GFF::Aggregator::gene - Sequence Ontology Geene
Bio::DB::GFF::Aggregator::match - Match aggregator
Bio::DB::GFF::Aggregator::orf - An aggregator for orf regions
Bio::DB::GFF::Aggregator::processed_transcript - Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::so_transcript - Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::transcript - Transcript aggregator
Bio::DB::GFF::Aggregator::ucsc_acembly - UCSC acembly aggregator
Bio::DB::GFF::Aggregator::ucsc_ensgene - UCSC ensGene aggregator
Bio::DB::GFF::Aggregator::ucsc_genscan - UCSC genscan aggregator
Bio::DB::GFF::Aggregator::ucsc_refgene - UCSC refGene aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22 - UCSC sanger22 aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo - UCSC sanger22pseudo aggregator
Bio::DB::GFF::Aggregator::ucsc_softberry - UCSC softberry aggregator
Bio::DB::GFF::Aggregator::ucsc_twinscan - UCSC twinscan aggregator
Bio::DB::GFF::Aggregator::ucsc_unigene - UCSC UniGene aggregator
Bio::DB::GFF::Featname - The name of a feature
Bio::DB::GFF::Feature - A relative segment identified by a feature type
Bio::DB::GFF::Homol - A segment of DNA that is homologous to another
Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support
Bio::DB::GFF::Segment - Simple DNA segment object
Bio::DB::GFF::Typename - The name of a feature type
Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
Bio::DB::GFF::Util::Rearrange - rearrange utility
Bio::DB::GenBank - Database object interface to GenBank
Bio::DB::GenPept - Database object interface to GenPept
Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.
Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database
Bio::DB::HIV::HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams
Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery
Bio::DB::InMemoryCache - Abstract interface for a sequence database
Bio::DB::IndexedBase - Base class for modules using indexed sequence files
Bio::DB::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
Bio::DB::MeSH - Term retrieval from a Web MeSH database
Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.
Bio::DB::Qual - Fast indexed access to quality files
Bio::DB::Query::GenBank - Build a GenBank Entrez Query
Bio::DB::Query::HIVQuery - Query interface to the Los Alamos HIV Sequence Database
Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies
Bio::DB::QueryI - Object Interface to queryable sequence databases
Bio::DB::RandomAccessI - Abstract interface for a sequence database
Bio::DB::RefSeq - Database object interface for RefSeq retrieval
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::NormalizedFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::NormalizedFeatureI - Interface for normalized features
Bio::DB::SeqFeature::NormalizedTableFeatureI - Interface for normalized features whose hierarchy is stored in a table
Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data
Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
Bio::DB::SeqFeature::Store::DBI::Iterator - utility methods for creating and iterating over SeqFeature records
Bio::DB::SeqFeature::Store::DBI::Pg - PostgreSQL implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::SQLite - SQLite implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::mysql - Mysql implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::FeatureFileLoader - feature file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF2Loader - GFF2 file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF3Loader - GFF3 file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::bdb - fetch and store objects from a BerkeleyDB
Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::DB::SeqFeature::Store::berkeleydb3 - Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::DB::SeqFeature::Store::memory - In-memory implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqHound - Database object interface to SeqHound
Bio::DB::SeqI - Abstract Interface for Sequence databases
Bio::DB::SeqVersion - front end to querying databases for identifier versions
Bio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History page
Bio::DB::SwissProt - Database object interface to SwissProt retrieval
Bio::DB::TFBS - Access to a Transcription Factor Binding Site database
Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
Bio::DB::Taxonomy - Access to a taxonomy database
Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver
Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files
Bio::DB::Taxonomy::greengenes - Use the Greengenes taxonomy
Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
Bio::DB::Taxonomy::silva - Use the Silva taxonomy
Bio::DB::Universal - Artificial database that delegates to specific databases
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences
Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references
Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types
Bio::Das::SegmentI - DAS-style access to a feature database
Bio::DasI - DAS-style access to a feature database
Bio::DescribableI - interface for objects with human readable names and descriptions
Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs
Bio::Event::EventGeneratorI - This interface describes the basic event generator class.
Bio::Event::EventHandlerI - An Event Handler Interface
Bio::Factory::AnalysisI - An interface to analysis tool factory
Bio::Factory::ApplicationFactoryI - Interface class for Application Factories
Bio::Factory::DriverFactory - Base class for factory classes loading drivers
Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string
Bio::Factory::MapFactoryI - A Factory for getting markers
Bio::Factory::ObjectBuilderI - Interface for an object builder
Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory
Bio::Factory::ObjectFactoryI - A General object creator factory
Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Bio::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms
Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream
Bio::FeatureHolderI - the base interface an object with features must implement
Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers).
Bio::IdCollectionI - interface for objects with multiple identifiers
Bio::IdentifiableI - interface for objects with identifiers
Bio::Index::Abstract - Abstract interface for indexing a flat file
Bio::Index::AbstractSeq - base class for AbstractSeq
Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
Bio::Index::BlastTable - Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
Bio::Index::Fastq - Interface for indexing (multiple) fastq files
Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query
Bio::Index::Qual - Interface for indexing (multiple) fasta qual files
Bio::Index::SwissPfam - Interface for indexing swisspfam files
Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.
Bio::LiveSeq::AARange - AARange abstract class for LiveSeq
Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl
Bio::LiveSeq::ChainI - Double linked chain data structure
Bio::LiveSeq::DNA - DNA object for LiveSeq
Bio::LiveSeq::Exon - Range abstract class for LiveSeq
Bio::LiveSeq::Gene - Range abstract class for LiveSeq
Bio::LiveSeq::IO::BioPerl - Loader for LiveSeq from EMBL entries with BioPerl
Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq
Bio::LiveSeq::Intron - Range abstract class for LiveSeq
Bio::LiveSeq::Mutation - Mutation event descriptor class
Bio::LiveSeq::Mutator - Package mutating LiveSequences
Bio::LiveSeq::Prim_Transcript - Prim_Transcript class for LiveSeq
Bio::LiveSeq::Range - Range abstract class for LiveSeq
Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq
Bio::LiveSeq::Repeat_Unit - Repeat_Unit class for LiveSeq
Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq
Bio::LiveSeq::Transcript - Transcript class for LiveSeq
Bio::LiveSeq::Translation - Translation class for LiveSeq
Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations
Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location
Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Bio::Location::Simple - Implementation of a Simple Location on a Sequence
Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Bio::LocationI - Abstract interface of a Location on a Sequence
Bio::Map::Clone - An central map object representing a clone
Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as FPC)
Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
Bio::Map::CytoMarker - An object representing a marker.
Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes
Bio::Map::EntityI - An Entity Interface
Bio::Map::FPCMarker - An central map object representing a marker
Bio::Map::Gene - An gene modelled as a mappable element.
Bio::Map::GeneMap - A MapI implementation to represent the area around a gene
Bio::Map::GenePosition - A typed position, suitable for modelling the various regions of a gene.
Bio::Map::GeneRelative - Represents being relative to named sub-regions of a gene.
Bio::Map::LinkageMap - A representation of a genetic linkage map.
Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
Bio::Map::MapI - Interface for describing Map objects in bioperl
Bio::Map::Mappable - An object representing a generic map element that can have multiple locations in several maps.
Bio::Map::MappableI - An object that can be placed in a map
Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps.
Bio::Map::MarkerI - Interface for basic marker functionality
Bio::Map::Microsatellite - An object representing a Microsatellite marker.
Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.
Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.
Bio::Map::Physical - A class for handling a Physical Map (such as FPC)
Bio::Map::Position - A single position of a Marker, or the range over which that marker lies, in a Map
Bio::Map::PositionHandler - A Position Handler Implementation
Bio::Map::PositionHandlerI - A Position Handler Interface
Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map
Bio::Map::PositionWithSequence - A position with a sequence.
Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps.
Bio::Map::Relative - Represents what a Position's coordiantes are relative to.
Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are relative to.
Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map
Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable element
Bio::MapIO - A Map Factory object
Bio::MapIO::fpc - A FPC Map reader
Bio::MapIO::mapmaker - A Mapmaker Map reader
Bio::Matrix::Generic - A generic matrix implementation
Bio::Matrix::IO - A factory for Matrix parsing
Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies
Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies
Bio::Matrix::MatrixI - An interface for describing a Matrix
Bio::Matrix::Mlagan - A generic matrix with mlagan fields
Bio::Matrix::PSM::IO - PSM parser
Bio::Matrix::PSM::IO::mast - PSM mast parser implementation
Bio::Matrix::PSM::IO::masta - motif fasta format parser
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
Bio::Matrix::PSM::IO::psiblast - PSM psiblast parser
Bio::Matrix::PSM::IO::transfac - PSM transfac parser
Bio::Matrix::PSM::InstanceSite - A PSM site occurance
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
Bio::Matrix::PSM::ProtPsm - handle combination of site matricies
Bio::Matrix::PSM::Psm - handle combination of site matricies
Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation
Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file
Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PSM::SiteMatrixI - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
Bio::Matrix::Scoring - Object which can hold scoring matrix information
Bio::MolEvol::CodonModel - Codon Evolution Models
Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
Bio::NexmlIO - stream handler for NeXML documents
Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name.
Bio::Ontology::GOterm - representation of GO terms
Bio::Ontology::InterProTerm - Implementation of InterProI term interface
Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
Bio::Ontology::OBOterm - representation of OBO terms
Bio::Ontology::Ontology - standard implementation of an Ontology
Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy
Bio::Ontology::OntologyI - Interface for an ontology implementation
Bio::Ontology::OntologyStore - A repository of ontologies
Bio::Ontology::Path - a path for an ontology term graph
Bio::Ontology::PathI - Interface for a path between ontology terms
Bio::Ontology::Relationship - a relationship for an ontology
Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms
Bio::Ontology::RelationshipType - a relationship type for an ontology
Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine
Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface
Bio::Ontology::Term - implementation of the interface for ontology terms
Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
Bio::Ontology::TermI - interface for ontology terms
Bio::OntologyIO - Parser factory for Ontology formats
Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database
Bio::OntologyIO::InterProParser - Parser for InterPro xml files.
Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats
Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format
Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium
Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats
Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format
Bio::ParameterBaseI - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
Bio::Perl - Functional access to BioPerl for people who don't know objects
Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species
Bio::Phenotype::MeSH::Twig - Context for a MeSH term
Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets
Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry
Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries
Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database
Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database
Bio::Phenotype::Phenotype - A class for modeling phenotypes
Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes
Bio::PhyloNetwork - Module to compute with Phylogenetic Networks
Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks
Bio::PhyloNetwork::FactoryX - Module to sequentially generate Phylogenetic Networks
Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz
Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks
Bio::PhyloNetwork::TreeFactory - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::TreeFactoryMulti - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::TreeFactoryX - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::muVector - Module to compute with vectors of arbitrary dimension
Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container
Bio::PopGen::GenotypeI - A marker and alleles for a specific individual
Bio::PopGen::IO - Input individual,marker,allele information
Bio::PopGen::IO::hapmap - A parser for HapMap output data
Bio::PopGen::IO::phase - A parser for Phase format data
Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format
Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results
Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results
Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes
Bio::PopGen::MarkerI - A Population Genetic conceptual marker
Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations
Bio::PopGen::Population - A population of individuals
Bio::PopGen::PopulationI - Interface for Populations
Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory
Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation
Bio::PopGen::Statistics - Population Genetics statistical tests
Bio::PopGen::TagHaplotype - Haplotype tag object.
Bio::PopGen::Utilities - Utilities for working with PopGen data and objects
Bio::PrimarySeq - Bioperl lightweight sequence object
Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
Bio::PullParserI - A base module for fast 'pull' parsing
Bio::Range - Pure perl RangeI implementation
Bio::RangeI - Range interface
Bio::Restriction::Analysis - cutting sequences with restriction enzymes
Bio::Restriction::Enzyme - A single restriction endonuclease (cuts DNA at specific locations)
Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease
Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease
Bio::Restriction::EnzymeCollection - Set of restriction endonucleases
Bio::Restriction::EnzymeI - Interface class for restriction endonuclease
Bio::Restriction::IO - Handler for sequence variation IO Formats
Bio::Restriction::IO::bairoch - bairoch enzyme set
Bio::Restriction::IO::base - base enzyme set
Bio::Restriction::IO::itype2 - itype2 enzyme set
Bio::Restriction::IO::prototype - prototype enzyme set
Bio::Restriction::IO::withrefm - withrefm enzyme set
Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable
Bio::Search::BlastStatistics - An object for Blast statistics
Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI - Interface for a database used in a sequence search
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::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::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::SearchDist - A perl wrapper around Sean Eddy's histogram object
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::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
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::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
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::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::SeqWithQuality - Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!
Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
Bio::Seq::SimulatedRead - Read with sequencing errors taken from a reference sequence
Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace
Bio::SeqAnalysisParserI - Sequence analysis output parser interface
Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations
Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes
Bio::SeqFeature::Amplicon - Amplicon feature
Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation
Bio::SeqFeature::Collection - 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 - An interface for a collection of SeqFeatureI objects.
Bio::SeqFeature::Computation - Computation SeqFeature
Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
Bio::SeqFeature::Gene::Exon - a feature representing an exon
Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::Intron - An intron feature
Bio::SeqFeature::Gene::NC_Feature - superclass for non-coding features
Bio::SeqFeature::Gene::Promoter - Describes a promoter
Bio::SeqFeature::Gene::Transcript - A feature representing a transcript
Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit
Bio::SeqFeature::Generic - Generic SeqFeature
Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class
Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature
Bio::SeqFeature::Primer - Primer Generic SeqFeature
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs
Bio::SeqFeature::Similarity - A sequence feature based on similarity
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences.
Bio::SeqFeature::SubSeq - Feature representing a subsequence
Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-gtprimary_tag
Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-gtprimary_tag
Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
Bio::SeqFeatureI - Abstract interface of a Sequence Feature
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqIO - Handler for SeqIO Formats
Bio::SeqIO::FTHelper - Helper class for EMBL/Genbank feature tables
Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
Bio::SeqIO::abi - abi trace sequence input/output stream
Bio::SeqIO::ace - ace sequence input/output stream
Bio::SeqIO::agave - AGAVE sequence output stream.
Bio::SeqIO::alf - alf trace sequence input/output stream
Bio::SeqIO::asciitree - asciitree sequence input/output stream
Bio::SeqIO::bsml - BSML sequence input/output stream
Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX
Bio::SeqIO::chadoxml - chadoxml sequence output stream
Bio::SeqIO::chaos - chaos sequence input/output stream
Bio::SeqIO::chaosxml - chaosxml sequence input/output stream
Bio::SeqIO::ctf - ctf trace sequence input/output stream
Bio::SeqIO::embl - EMBL sequence input/output stream
Bio::SeqIO::embldriver - EMBL sequence input/output stream
Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser
Bio::SeqIO::excel - sequence input/output stream from a MSExcel-formatted table
Bio::SeqIO::exp - exp trace sequence input/output stream
Bio::SeqIO::fasta - fasta sequence input/output stream
Bio::SeqIO::fastq - fastq sequence input/output stream
Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream
Bio::SeqIO::game - a class for parsing and writing game-XML
Bio::SeqIO::game::featHandler - a class for handling feature elements
Bio::SeqIO::game::gameHandler - PerlSAX handler for game-XML
Bio::SeqIO::game::gameSubs - a base class for game-XML parsing
Bio::SeqIO::game::gameWriter - a class for writing game-XML
Bio::SeqIO::game::seqHandler - a class for handling game-XML sequences
Bio::SeqIO::gbdriver - GenBank handler-based push parser
Bio::SeqIO::gbxml - GenBank sequence input/output stream using SAX
Bio::SeqIO::gcg - GCG sequence input/output stream
Bio::SeqIO::genbank - GenBank sequence input/output stream
Bio::SeqIO::interpro - InterProScan XML input/output stream
Bio::SeqIO::kegg - KEGG sequence input/output stream
Bio::SeqIO::largefasta - method i/o on very large fasta sequence files
Bio::SeqIO::lasergene - Lasergene sequence file input/output stream
Bio::SeqIO::locuslink - LocusLink input/output stream
Bio::SeqIO::mbsout - input stream for output by Teshima et al.'s mbs.
Bio::SeqIO::metafasta - metafasta sequence input/output stream
Bio::SeqIO::msout - input stream for output by Hudson's ms
Bio::SeqIO::nexml - NeXML sequence input/output stream
Bio::SeqIO::phd - phd file input/output stream
Bio::SeqIO::pir - PIR sequence input/output stream
Bio::SeqIO::pln - pln trace sequence input/output stream
Bio::SeqIO::qual - .qual file input/output stream
Bio::SeqIO::raw - raw sequence file input/output stream
Bio::SeqIO::scf - .scf file input/output stream
Bio::SeqIO::seqxml - SeqXML sequence input/output stream
Bio::SeqIO::strider - DNA strider sequence input/output stream
Bio::SeqIO::swiss - Swissprot sequence input/output stream
Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser
Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
Bio::SeqIO::table - sequence input/output stream from a delimited table
Bio::SeqIO::tigr - TIGR XML sequence input/output stream
Bio::SeqIO::tigrxml - Parse TIGR (new) XML
Bio::SeqIO::tinyseq - reading/writing sequences in NCBI TinySeq format
Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing
Bio::SeqIO::ztr - ztr trace sequence input/output stream
Bio::SeqUtils - Additional methods for PrimarySeq objects
Bio::SimpleAlign - Multiple alignments held as a set of sequences
Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool
Bio::Species - Generic species object.
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
Bio::Structure::Chain - Bioperl structure Object, describes a chain
Bio::Structure::Entry - Bioperl structure Object, describes the whole entry
Bio::Structure::IO - Handler for Structure Formats
Bio::Structure::IO::pdb - PDB input/output stream
Bio::Structure::Model - Bioperl structure Object, describes a Model
Bio::Structure::Residue - Bioperl structure Object, describes a Residue
Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output
Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output
Bio::Structure::StructureI - Abstract Interface for a Structure objects
Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet
Bio::Symbol::AlphabetI - A Symbol Alphabet
Bio::Symbol::DNAAlphabet - A ready made DNA alphabet
Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
Bio::Symbol::Symbol - A biological symbol
Bio::Symbol::SymbolI - Interface for a Symbol
Bio::Taxon - A node in a represented taxonomy
Bio::Taxonomy - representing Taxonomy.
Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
Bio::Taxonomy::Node - A node in a represented taxonomy
Bio::Taxonomy::Taxon - Generic Taxonomic Entity object
Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface.
Bio::Tools::AlignFactory - Base object for alignment factories
Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files
Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality.
Bio::Tools::AmpliconSearch - Find amplicons in a template using degenerate PCR primers
Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server
Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server
Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein secondary structure prediction server
Bio::Tools::Analysis::Protein::HNN - a wrapper around the HNN protein secondary structure prediction server
Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server
Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server
Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server
Bio::Tools::Analysis::Protein::Sopma - a wrapper around the Sopma protein secondary structure prediction server
Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations
Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers
Bio::Tools::Blat - parser for Blat program
Bio::Tools::CodonTable - Codon table object
Bio::Tools::Coil - parser for Coil output
Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
Bio::Tools::EPCR - Parse ePCR output and make features
Bio::Tools::ERPIN - a parser for ERPIN output
Bio::Tools::ESTScan - Results of one ESTScan run
Bio::Tools::Eponine - Results of one Eponine run
Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
Bio::Tools::Fgenesh - parse results of one Fgenesh run
Bio::Tools::FootPrinter - write sequence features in FootPrinter format
Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
Bio::Tools::Gel - Calculates relative electrophoretic migration distances
Bio::Tools::Geneid - Results of one geneid run
Bio::Tools::Genemark - Results of one Genemark run
Bio::Tools::Genewise - Results of one Genewise run
Bio::Tools::Genomewise - Results of one Genomewise run
Bio::Tools::Genscan - Results of one Genscan run
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
Bio::Tools::Grail - Results of one Grail run
Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Bio::Tools::HMMER::Domain - One particular domain hit from HMMER
Bio::Tools::HMMER::Results - Object representing HMMER output results
Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches
Bio::Tools::Hmmpfam - Parser for Hmmpfam program
Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
Bio::Tools::Infernal - A parser for Infernal output
Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Bio::Tools::MZEF - Results of one MZEF run
Bio::Tools::Match - Parses output from Transfac's match(TM)
Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence
Bio::Tools::Phylo::Gerp - Parses output from GERP
Bio::Tools::Phylo::Gumby - Parses output from gumby
Bio::Tools::Phylo::Molphy - parser for Molphy output
Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run
Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml.
Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML
Bio::Tools::Phylo::PAML::Result - A PAML result set object
Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output
Bio::Tools::Prediction::Exon - A predicted exon feature
Bio::Tools::Prediction::Gene - a predicted gene structure feature
Bio::Tools::Primer3 - Create input for and work with the output from the program primer3
Bio::Tools::Primer::Assessor::Base - base class for common assessor things
Bio::Tools::Primer::AssessorI - interface for assessing primer pairs
Bio::Tools::Primer::Feature - position of a single primer
Bio::Tools::Primer::Pair - two primers on left and right side
Bio::Tools::Prints - Parser for FingerPRINTScanII program
Bio::Tools::Profile - parse Profile output
Bio::Tools::Promoterwise - parser for Promoterwise tab format output
Bio::Tools::PrositeScan - Parser for ps_scan result
Bio::Tools::Protparam - submit to and parse output from protparam ;
Bio::Tools::Pseudowise - Results of one Pseudowise run
Bio::Tools::QRNA - A Parser for qrna output
Bio::Tools::RNAMotif - A parser for RNAMotif output
Bio::Tools::RandomDistFunctions - A set of routines useful for generating random data in different distributions
Bio::Tools::RepeatMasker - a parser for RepeatMasker output
Bio::Tools::Run::GenericParameters - An object for the parameters used to run programs
Bio::Tools::Run::ParametersI - A Base object for the parameters used to run programs
Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP
Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
Bio::Tools::Run::StandAloneNCBIBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
Bio::Tools::Run::StandAloneWUBlast - Object for the local execution of WU-Blast.
Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
Bio::Tools::Seg - parse seg output
Bio::Tools::SeqPattern - represent a sequence pattern or motif
Bio::Tools::SeqStats - Object holding statistics for one particular sequence
Bio::Tools::SeqWords - Object holding n-mer statistics for a sequence
Bio::Tools::SiRNA - Perl object for designing small inhibitory RNAs.
Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis
Bio::Tools::Signalp - parser for Signalp output
Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp output
Bio::Tools::Sim4::Exon - A single exon determined by an alignment
Bio::Tools::Sim4::Results - Results of one Sim4 run
Bio::Tools::Spidey::Exon - A single exon determined by an alignment
Bio::Tools::Spidey::Results - Results of a Spidey run
Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output
Bio::Tools::TargetP - Results of one TargetP run
Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment
Bio::Tools::ipcress - Parse ipcress output and make features
Bio::Tools::isPcr - Parse isPcr output and make features
Bio::Tools::pICalculator - calculate the isoelectric point of a protein
Bio::Tools::pSW - pairwise Smith Waterman object
Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
Bio::Tree::AlleleNode - A Node with Alleles attached
Bio::Tree::AnnotatableNode - A Tree Node with support for annotation
Bio::Tree::Compatible - Testing compatibility of phylogenetic trees with nested taxa.
Bio::Tree::DistanceFactory - Construct a tree using distance based methods
Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
Bio::Tree::Node - A Simple Tree Node
Bio::Tree::NodeI - Interface describing a Tree Node
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
Bio::Tree::RandomFactory - TreeFactory for generating Random Trees
Bio::Tree::Statistics - Calculate certain statistics for a Tree
Bio::Tree::Tree - An implementation of the TreeI interface.
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Bio::TreeIO - Parser for Tree files
Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
Bio::TreeIO::lintree - Parser for lintree output trees
Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.
Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output
Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
Bio::Variation::AAChange - Sequence change class for polypeptides
Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes
Bio::Variation::Allele - Sequence object with allele-specific attributes
Bio::Variation::DNAMutation - DNA level mutation class
Bio::Variation::IO - Handler for sequence variation IO Formats
Bio::Variation::IO::flat - flat file sequence variation input/output stream
Bio::Variation::IO::xml - XML sequence variation input/output stream
Bio::Variation::RNAChange - Sequence change class for RNA level
Bio::Variation::SNP - submitted SNP
Bio::Variation::SeqDiff - Container class for mutation/variant descriptions
Bio::Variation::VariantI - Sequence Change SeqFeature abstract class
Bio::WebAgent - A base class for Web (any protocol) access
Provides
Bio::AnalysisI::JobI in Bio/AnalysisI.pm
Bio::Coordinate::Chain in Bio/Coordinate/Chain.pm
Bio::Coordinate::Collection in Bio/Coordinate/Collection.pm
Bio::Coordinate::ExtrapolatingPair in Bio/Coordinate/ExtrapolatingPair.pm
Bio::Coordinate::GeneMapper in Bio/Coordinate/GeneMapper.pm
Bio::Coordinate::Graph in Bio/Coordinate/Graph.pm
Bio::Coordinate::MapperI in Bio/Coordinate/MapperI.pm
Bio::Coordinate::Pair in Bio/Coordinate/Pair.pm
Bio::Coordinate::Result in Bio/Coordinate/Result.pm
Bio::Coordinate::Result::Gap in Bio/Coordinate/Result/Gap.pm
Bio::Coordinate::Result::Match in Bio/Coordinate/Result/Match.pm
Bio::Coordinate::ResultI in Bio/Coordinate/ResultI.pm
Bio::Coordinate::Utils in Bio/Coordinate/Utils.pm
Bio::DB::Fasta::Subdir in Bio/DB/SeqFeature/Store/berkeleydb.pm
Bio::DB::GFF::Adaptor::dbi::faux_dbh in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio::DB::GFF::ID_Iterator in Bio/DB/GFF.pm
Bio::DB::Indexed::Stream in Bio/DB/IndexedBase.pm
Bio::DB::SeqFeature::Store::berkeleydb::Iterator in Bio/DB/SeqFeature/Store/berkeleydb.pm
Bio::DB::SeqFeature::Store::FeatureIterator in Bio/DB/SeqFeature/Store.pm
Bio::DB::SeqFeature::Store::memory::Iterator in Bio/DB/SeqFeature/Store/memory.pm
Bio::LocatableSeq in Bio/Search/Tiling/MapTileUtils.pm
Bio::PrimarySeq::Fasta in Bio/DB/Fasta.pm
Bio::Root::Build in Bio/Root/Build.pm
Bio::Root::Exception in Bio/Root/Exception.pm
Bio::Root::IO in Bio/Root/IO.pm
Bio::Root::Root in Bio/Root/Root.pm
Bio::Root::RootI in Bio/Root/RootI.pm
Bio::Root::Storable in Bio/Root/Storable.pm
Bio::Root::Test in Bio/Root/Test.pm
Bio::Root::Utilities in Bio/Root/Utilities.pm
Bio::Root::Version in Bio/Root/Version.pm
Bio::Search::HSP::HSPI in Bio/Search/Tiling/MapTileUtils.pm
Bio::Seq::PrimaryQual::Qual in Bio/DB/Qual.pm
FeatureStore in Bio/DB/GFF/Adaptor/berkeleydb.pm
Examples



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