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bioperl-1.0.2
++

Changes for version 1.0.2

  • o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided in this release will not work after December 2002 when NCBI shuts off the old Entrez cgi scripts. We have already fixed on our main development branch and the functionality will be available in the next stable bioperl release (1.2) slated for Fall 2002.
  • o Numerous parsing bugs in Bio::SearchIO::fasta found through testset by Robin Emig. These were fixed as was the get_aln method in Bio::Search::HSP::GenericHSP to handle the extra context sequence that is provided with a FastA alignment.
  • o Migrating differences between Bio::Search::XX::BlastXX to Bio::Search::XX::GenericXX objects. This included mechanism to retrieve whole list of HSPs from Hits and whole list of Hits from Results in addition to the current next_XX iterator methods that are available. Added seq_inds() method to GenericHSP which identifies indexes in the query or hit sequences where conserved,identical,gaps, or mismatch residues are located (adapted from Steve Chervitz's implementation in BlastHSP).
  • o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release. Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
  • o Bio::Graphics glyph set improved and extended for GBrowse release
  • o Bio::Tree::Tree get_nodes implementation improvement thanks to Howard Ross notice performance problem when writing out unbalanced trees.
  • o Bio::Location::Fuzzy::new named parameter -loc_type became -location_type, Bio::Location::Simple::new named parameter -seqid becamse -seq_id.
  • o Fixed major Bio::AlignIO::emboss parsing bug on needle output, was mis-detecting that gaps should be placed at the beginning of the alignment when the best alignment starts internally in the sequence.

Documentation

Bioperl
biodesign.pod
Bioperl Design Documentation
Bioperl
Coordinated OOP-Perl Modules for Biology
BioPerlTutorial
a tutorial for bioperl
gadfly_to_gff.pl
Massage Gadfly's GFF format into a form suitable for Bio::DB::GFF
sgd_to_gff.pl
Massage SGD's feature dump format into a form suitable for Bio::DB::GFF
dbfetch
generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
bpfetch.pl
fetches sequences from bioperl indexed databases
bpindex.pl
indexes files for use by bpfetch
feature_draw.pl
Render a Bio::Graphics Feature File
gff2ps
you will want to change this script

Modules

Bio::Align::AlignI
An interface for describing sequence alignments.
Bio::AlignIO
Handler for AlignIO Formats
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 sequence input/output 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::msf
msf sequence input/output stream
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::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::AnalysisParserI
Generic analysis output parser interface
Bio::AnalysisResultI
Interface for analysis result objects
Bio::Annotation
A generic object for annotations.
Bio::Annotation::Collection
Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment
A comment object, holding text
Bio::Annotation::DBLink
DESCRIPTION of Object
Bio::Annotation::Reference
Specialised DBLink object for Literature References
Bio::Annotation::SimpleValue
A simple scalar
Bio::Annotation::TypeManager
Manages types for annotation collections
Bio::AnnotationCollectionI
Interface for annotation collections
Bio::AnnotationI
Annotation interface
Bio::Biblio
A Bibliographic Query Service module
Bio::Biblio::Article
Representation of a general article
Bio::Biblio::BiblioBase
An abstract base for other biblio classes
Bio::Biblio::Book
Representation of a book
Bio::Biblio::BookArticle
Representation of a book article
Bio::Biblio::IO
Handling the bibliographic references
Bio::Biblio::IO::medline2ref
A converter of a raw hash to MEDLINE citations
Bio::Biblio::IO::medlinexml
A converter of XML files with MEDLINE citations
Bio::Biblio::IO::pubmed2ref
A converter of a raw hash to PUBMED citations
Bio::Biblio::IO::pubmedxml
A converter of XML files with PUBMED citations
Bio::Biblio::Journal
Representation of a journal
Bio::Biblio::JournalArticle
Representation of a journal article
Bio::Biblio::MedlineArticle
Representation of a MEDLINE article
Bio::Biblio::MedlineBook
Representation of a MEDLINE book
Bio::Biblio::MedlineBookArticle
Representation of a MEDLINE book article
Bio::Biblio::MedlineJournal
Representation of a MEDLINE journal
Bio::Biblio::MedlineJournalArticle
Representation of a MEDLINE journal article
Bio::Biblio::Organisation
Representation of an organisation
Bio::Biblio::Patent
Representation of a patent
Bio::Biblio::Person
Representation of a person
Bio::Biblio::Proceeding
Representation of a conference proceeding
Bio::Biblio::Provider
Representation of a general provider
Bio::Biblio::PubmedArticle
Representation of a PUBMED article
Bio::Biblio::PubmedBookArticle
Representation of a PUBMED book article
Bio::Biblio::PubmedJournalArticle
Representation of a PUBMED journal article
Bio::Biblio::Ref
Representation of a bibliographic reference
Bio::Biblio::Service
Representation of a provider of type service
Bio::Biblio::TechReport
Representation of a technical report
Bio::Biblio::Thesis
Representation of thesis
Bio::Biblio::WebResource
Representation of a web resource
Bio::DB::Ace
Database object interface to ACeDB servers
Bio::DB::Biblio::biofetch
A BioFetch-based access to a bibliographic citation retrieval
Bio::DB::Biblio::soap
A SOAP-based access to a bibliographic query service
Bio::DB::BiblioI
An interface to a Bibliographic Query Service
Bio::DB::BioFetch
Database object interface to BioFetch retrieval
Bio::DB::DBFetch
Database object for retrieving using the dbfetch script
Bio::DB::EMBL
Database object interface for EMBL entry retrieval
Bio::DB::Failover
A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs
Bio::DB::Fasta
Fast indexed access to a directory of 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::OBDAIndex
Binary search indexing system for sequence files
Bio::DB::GDB
Database object interface to GDB HTTP query
Bio::DB::GFF
Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::biofetch
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::mysql
Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Optimized Bio::DB::GFF adaptor for mysql
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::none
No aggregation
Bio::DB::GFF::Aggregator::transcript
Transcript 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::GenBank
Database object interface to GenBank
Bio::DB::GenPept
Database object interface to GenPept
Bio::DB::InMemoryCache
Abstract interface for a sequence database
Bio::DB::NCBIHelper
A collection of routines useful for queries to NCBI databases.
Bio::DB::RandomAccessI
Abstract interface for a sequence database
Bio::DB::RefSeq
Database object interface for RefSeq retrieval
Bio::DB::Registry
Access to the Open Bio Database Access registry scheme
Bio::DB::SeqI
Abstract Interface for Sequence databases
Bio::DB::SwissProt
Database object interface to SwissProt retrieval
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::DB::XEMBL
Database object interface for XEMBL entry retrieval
Bio::DB::XEMBLService
SOAP service definition for XEMBL
Bio::DBLinkContainerI
Abstract interface for any object wanting to use database cross references
Bio::DasI
DAS-style access to a feature database
Bio::DasSegmentI
DAS-style access to a feature database
Bio::Event::EventGeneratorI
This interface describes the basic event generator class.
Bio::Event::EventHandlerI
An Event Handler Interface
Bio::Factory::ApplicationFactoryI
Interface class for Application Factories
Bio::Factory::BlastHitFactory
Factory for Bio::Search::Hit::BlastHit objects
Bio::Factory::BlastResultFactory
Factory for Bio::Search::Result::BlastResult objects
Bio::Factory::DriverFactory
Base class for factory classes loading drivers
Bio::Factory::EMBOSS
EMBOSS appliaction factory class
Bio::Factory::HitFactoryI
Interface for an object that builds Bio::Search::Hit::HitI objects
Bio::Factory::MapFactoryI
A Factory for getting markers
Bio::Factory::ResultFactoryI
Interface for an object that builds Bio::Search::Result::ResultI objects
Bio::Factory::SeqAnalysisParserFactory
class capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SeqAnalysisParserFactoryI
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::TreeFactoryI
Factory Interface for getting and writing trees from/to a data stream
Bio::Graphics
Generate GD images of Bio::Seq objects
Bio::Graphics::Feature
A simple feature object for use with Bio::Graphics::Panel
Bio::Graphics::FeatureFile
A set of Bio::Graphics features, stored in a file
Bio::Graphics::Glyph
Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::alignment
The "alignment" glyph
Bio::Graphics::Glyph::anchored_arrow
The "anchored_arrow" glyph
Bio::Graphics::Glyph::arrow
The "arrow" glyph
Bio::Graphics::Glyph::box
The "box" glyph
Bio::Graphics::Glyph::cds
The "cds" glyph
Bio::Graphics::Glyph::crossbox
The "crossbox" glyph
Bio::Graphics::Glyph::diamond
The "diamond" glyph
Bio::Graphics::Glyph::dna
The "dna" glyph
Bio::Graphics::Glyph::dot
The "dot" glyph
Bio::Graphics::Glyph::ellipse
The "ellipse" glyph
Bio::Graphics::Glyph::ex
The "crossbox" glyph
Bio::Graphics::Glyph::extending_arrow
The "extending arrow" glyph
Bio::Graphics::Glyph::generic
The "generic" glyph
Bio::Graphics::Glyph::graded_segments
The "graded_segments" glyph
Bio::Graphics::Glyph::group
The "group" glyph
Bio::Graphics::Glyph::heterogeneous_segments
The "heterogeneous_segments" glyph
Bio::Graphics::Glyph::line
The "line" glyph
Bio::Graphics::Glyph::oval
The "oval" glyph
Bio::Graphics::Glyph::pinsertion
The "Drosophila P-element Insertion" glyph
Bio::Graphics::Glyph::primers
The "STS primers" glyph
Bio::Graphics::Glyph::rndrect
The "round rect" glyph
Bio::Graphics::Glyph::ruler_arrow
The "ruler_arrow" glyph
Bio::Graphics::Glyph::segmented_keyglyph
The "segmented_keyglyph" glyph
Bio::Graphics::Glyph::segments
The "segments" glyph
Bio::Graphics::Glyph::span
The "span" glyph
Bio::Graphics::Glyph::toomany
The "too many to show" glyph
Bio::Graphics::Glyph::track
The "track" glyph
Bio::Graphics::Glyph::transcript
The "transcript" glyph
Bio::Graphics::Glyph::transcript2
The "transcript2" glyph
Bio::Graphics::Glyph::translation
The "6-frame translation" glyph
Bio::Graphics::Glyph::triangle
The "triangle" glyph
Bio::Graphics::Panel
Generate GD images of Bio::Seq objects
Bio::Index::Abstract
Abstract interface for indexing a flat file
Bio::Index::AbstractSeq
Base class for AbstractSeq s
Bio::Index::Blast
Indexes Blast reports and supports retrieval based on query accession(s)
Bio::Index::EMBL
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie 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 (multiple) GenBank .seq files (ie flat file GenBank format).
Bio::Index::SwissPfam
Interface for indexing swisspfam files
Bio::Index::Swissprot
Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).
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::IO::SRS
Loader for LiveSeq from EMBL entries with SRS
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::LocatableSeq
A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
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::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::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::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::Position
A single position of a Marker in a Map
Bio::Map::PositionI
Abstracts the notion of a position having a value in the context of a marker and a Map
Bio::Map::SimpleMap
A MapI implementation handling the basics of a Map
Bio::MapIO
A Map Factory object
Bio::MapIO::mapmaker
A Mapmaker Map reader
Bio::Perl
Functional access to BioPerl for people who don't know objects
Bio::PrimarySeq
Bioperl lightweight Sequence Object
Bio::PrimarySeqI
Interface definition for a Bio::PrimarySeq
Bio::Range
Pure perl RangeI implementation
Bio::RangeI
Range interface
Bio::Root::Err
Exception class for Perl 5 objects
Bio::Root::Exception
Generic exception objects for Bioperl
Bio::Root::Global
Global variables and utility functions
Bio::Root::HTTPget
module for fallback HTTP get operations when LWP:: is unavailable
Bio::Root::IO
module providing several methods often needed when dealing with file IO
Bio::Root::IOManager
Input and output manager for Perl5 objects.
Bio::Root::Object
A core Perl 5 object.
Bio::Root::Root
Hash-based implementation of Bio::Root::RootI
Bio::Root::RootI
Abstract interface to root object code
Bio::Root::Utilities
General-purpose utility module
Bio::Root::Vector
Interface for managing linked lists of Perl5 objects.
Bio::Root::Xref
A generic cross-reference object.
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::HSP::BlastHSP
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::GenericHSP
DESCRIPTION of Object
Bio::Search::HSP::HSPI
Interface for a High Scoring Pair in a similarity search result
Bio::Search::Hit::BlastHit
Bioperl BLAST Hit object
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::HitI
Interface for a hit in a similarity search result
Bio::Search::Result::BlastResult
A top-level BLAST Report object
Bio::Search::Result::GenericResult
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
Bio::Search::Result::ResultI
Abstract interface to Search Result objects
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::SearchResultEventBuilder
Event Handler for SearchIO events.
Bio::SearchIO::SearchWriterI
Interface for outputting parsed Search results
Bio::SearchIO::Writer::HSPTableWriter
Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HTMLResultWriter
Object to implement writing 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::blast
Event generator for event based parsing of blast reports
Bio::SearchIO::blastxml
A SearchIO implementation of NCBI Blast XML parsing.
Bio::SearchIO::fasta
A SearchIO parser for FASTA results
Bio::SearchIO::psiblast
Parser for traditional BLAST and PSI-BLAST reports
Bio::Seq
Sequence object, with features
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::PrimaryQual
Bioperl lightweight Quality Object
Bio::Seq::QualI
Interface definition for a Bio::Seq::Qual
Bio::Seq::RichSeq
Module implementing a sequence created from a rich sequence database entry
Bio::Seq::RichSeqI
RichSeq interface, mainly for database orientated sequences
Bio::Seq::SeqWithQuality
Bioperl object packaging a sequence with its quality
Bio::SeqAnalysisParserI
Sequence analysis output parser interface
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
DESCRIPTION of Object
Bio::SeqFeature::Gene::NC_Feature
DESCRIPTION of Object
Bio::SeqFeature::Gene::Poly_A_site
DESCRIPTION of Object
Bio::SeqFeature::Gene::Promoter
DESCRIPTION of Object
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 transcription unit
Bio::SeqFeature::Generic
Generic SeqFeature
Bio::SeqFeature::PositionProxy
Bio::SeqFeature::Similarity
A sequence feature based on similarity
Bio::SeqFeature::SimilarityPair
Sequence feature based on the similarity of two sequences.
Bio::SeqFeatureI
Abstract interface of a Sequence Feature
Bio::SeqI
Abstract Interface of Sequence (with features)
Bio::SeqIO
Handler for SeqIO Formats
Bio::SeqIO::FTHelper
Helper class for Embl/Genbank feature tables
Bio::SeqIO::MultiFile
Treating a set of files as a single input stream
Bio::SeqIO::ace
ace sequence input/output stream
Bio::SeqIO::bsml
BSML sequence input/output stream
Bio::SeqIO::embl
EMBL sequence input/output stream
Bio::SeqIO::fasta
fasta sequence input/output stream
Bio::SeqIO::fastq
fastq sequence input/output stream
Bio::SeqIO::game
Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.
Bio::SeqIO::game::featureHandler
GAME helper via PerlSAX helper.
Bio::SeqIO::game::idHandler
GAME helper via PerlSAX helper.
Bio::SeqIO::game::seqHandler
GAME helper via PerlSAX helper.
Bio::SeqIO::gcg
GCG sequence input/output stream
Bio::SeqIO::genbank
GenBank sequence input/output stream
Bio::SeqIO::largefasta
method i/o on very large fasta sequence files
Bio::SeqIO::phd
.phd file input/output stream
Bio::SeqIO::pir
PIR 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::swiss
Swissprot sequence input/output stream
Bio::SeqUtils
Additional methods for PrimarySeq objects
Bio::SimpleAlign
Multiple alignments held as a set of sequences
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
DESCRIPTION of Object
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::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::AnalysisResult
Base class for analysis result objects and parsers
Bio::Tools::BPbl2seq
Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Bio::Tools::BPlite
Lightweight BLAST parser
Bio::Tools::BPlite::HSP
Blast report High Scoring Pair (HSP)
Bio::Tools::BPlite::Iteration
object for parsing single iteration of a PSIBLAST report
Bio::Tools::BPlite::Sbjct
A Blast Subject (database search Hit)
Bio::Tools::BPpsilite
Bio::Tools::Blast
Bioperl BLAST sequence analysis object
Bio::Tools::Blast::HSP
Bioperl BLAST High-Scoring Segment Pair object
Bio::Tools::Blast::HTML
Bioperl Utility module for HTML formatting Blast reports
Bio::Tools::Blast::Sbjct
Bioperl BLAST "Hit" object
Bio::Tools::CodonTable
Bioperl codon table object
Bio::Tools::EPCR
Parse ePCR output and make features
Bio::Tools::ESTScan
Results of one ESTScan run
Bio::Tools::GFF
A Bio::SeqAnalysisParserI compliant GFF format parser
Bio::Tools::Gel
Calculates relative electrophoretic migration distances
Bio::Tools::Genemark
Results of one Genemark run
Bio::Tools::Genscan
Results of one Genscan run
Bio::Tools::Grail
Results of one Grail run
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::IUPAC
Generates unique Seq objects from an ambiguous Seq object
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::OddCodes
Object holding alternative alphabet coding for one protein sequence
Bio::Tools::Prediction::Exon
A predicted exon feature
Bio::Tools::Prediction::Gene
a predicted gene structure feature
Bio::Tools::RestrictionEnzyme
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
Bio::Tools::Run::Alignment::Clustalw
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Bio::Tools::Run::Alignment::TCoffee
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
Bio::Tools::Run::EMBOSSApplication
class for EMBOSS Applications
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)
Bio::Tools::SeqAnal
Bioperl sequence analysis base class.
Bio::Tools::SeqPattern
Bioperl object for a sequence pattern or motif
Bio::Tools::SeqStats
Object holding statistics for one particular sequence
Bio::Tools::SeqWords
Object holding n-mer statistics for one sequence
Bio::Tools::Sigcleave
Bioperl object for sigcleave analysis
Bio::Tools::Sim4::Exon
A single exon determined by an alignment
Bio::Tools::Sim4::Results
Results of one Sim4 run
Bio::Tools::StateMachine::AbstractStateMachine
Abstract state machine object
Bio::Tools::StateMachine::IOStateMachine
IO-based implementation of AbstractStateMachine
Bio::Tools::WWW
Bioperl manager for web resources related to biology.
Bio::Tools::pSW
pairwise Smith Waterman object
Bio::Tree::AlleleNode
DESCRIPTION of Object
Bio::Tree::Node
A Simple Tree Node
Bio::Tree::NodeI
Interface describing a Tree Node
Bio::Tree::RandomFactory
TreeFactory for generating Random Trees
Bio::Tree::Statistics
Calculate certain statistics for a Tree
Bio::Tree::Tree
An Implementation of TreeI interface.
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::newick
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
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::SeqDiff
Container class for mutation/variant descriptions
Bio::Variation::VariantI
Sequence Change SeqFeature abstract class
Bio::PrimarySeq
Bio::PrimarySeqI
Bio::Seq
Bio::SeqI
Error
TestInterface
TestObject

Provides

Bio::DB::Fasta::Stream
in Bio/DB/Fasta.pm
Bio::DB::Flat::BDB::embl
in Bio/DB/Flat/BDB/embl.pm
Bio::DB::Flat::BDB::fasta
in Bio/DB/Flat/BDB/fasta.pm
Bio::DB::GFF::Adaptor::dbi::faux_dbh
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio::DB::GFF::Adaptor::dbi::faux_sth
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio::DB::GFF::Adaptor::dbi::iterator
in Bio/DB/GFF/Adaptor/dbi/iterator.pm
Bio::DB::GFF::Adaptor::memory
in Bio/DB/GFF/Adaptor/memory.pm
Bio::DB::GFF::Adaptor::memory_iterator
in Bio/DB/GFF/Adaptor/memory_iterator.pm
Bio::DB::GFF::ID_Iterator
in Bio/DB/GFF.pm
Bio::DB::GFF::Util::Binning
in Bio/DB/GFF/Util/Binning.pm
Bio::DB::GFF::Util::Rearrange
in Bio/DB/GFF/Util/Rearrange.pm
Bio::Graphics::Glyph::Factory
in Bio/Graphics/Glyph/Factory.pm
Bio::Graphics::Util
in Bio/Graphics/Util.pm
Bio::PrimarySeq::Fasta
in Bio/DB/Fasta.pm

Examples

Other files