|
Bio::Align::AlignI
|
An interface for describing sequence alignments.
|
|
|
|
Bio::Align::DNAStatistics
|
Calculate some statistics for a DNA alignment
|
|
|
|
Bio::Align::PairwiseStatistics
|
Base statistic object for Pairwise Alignments
|
|
|
|
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::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::maf
|
Multipla 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::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::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
|
DESCRIPTION of Object
|
|
|
|
Bio::Annotation::OntologyTerm
|
An ontology term adapted to AnnotationI
|
|
|
|
Bio::Annotation::Reference
|
Specialised DBLink object for Literature References
|
|
|
|
Bio::Annotation::SimpleValue
|
A simple scalar
|
|
|
|
Bio::Annotation::StructuredValue
|
A scalar with embedded structured information
|
|
|
|
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 phrap ACE files.
|
|
|
|
Bio::Assembly::IO::phrap
|
driver to load phrap.out files.
|
|
|
|
Bio::Assembly::Scaffold
|
Perl module to hold and manipulate sequence assembly data.
|
|
|
|
Bio::Assembly::ScaffoldI
|
Abstract Inteface of Sequence Assemblies
|
|
|
|
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::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::Coordinate::Chain
|
Mapping locations through a chain of coordinate mappers
|
|
|
|
Bio::Coordinate::Collection
|
Noncontinuous match between two coordinate sets
|
|
|
|
Bio::Coordinate::ExtrapolatingPair
|
Continuous match between two coordinate sets
|
|
|
|
Bio::Coordinate::GeneMapper
|
transformations between gene related coordinate systems
|
|
|
|
Bio::Coordinate::Graph
|
Finds shortest path between nodes in a graph
|
|
|
|
Bio::Coordinate::MapperI
|
Interface describing coordinate mappers
|
|
|
|
Bio::Coordinate::Pair
|
Continuous match between two coordinate sets
|
|
|
|
Bio::Coordinate::Result
|
Results from coordinate transformation
|
|
|
|
Bio::Coordinate::Result::Gap
|
Another name for Bio::Location::Simple
|
|
|
|
Bio::Coordinate::Result::Match
|
Another name for Bio::Location::Simple
|
|
|
|
Bio::Coordinate::ResultI
|
Interface to identify coordinate mapper results
|
|
|
|
Bio::Coordinate::Utils
|
Additional methods to create Bio::Coordinate objects
|
|
|
|
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::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::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::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::BDB::swissprot
|
swissprot adaptor for Open-bio standard BDB-indexed flat file
|
|
|
|
Bio::DB::Flat::BinarySearch
|
BinarySearch 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::ace
|
ace interface (for multiple inheritance)
|
|
|
|
Bio::DB::GFF::Adaptor::biofetch
|
Cache BioFetch objects in a Bio::DB::GFF database
|
|
|
|
Bio::DB::GFF::Adaptor::biofetch_oracle
|
|
|
|
|
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::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::memory
|
|
|
|
|
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::match
|
Match aggregator
|
|
|
|
Bio::DB::GFF::Aggregator::none
|
No aggregation
|
|
|
|
Bio::DB::GFF::Aggregator::processed_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::InMemoryCache
|
Abstract interface for a sequence database
|
|
|
|
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::Query::GenBank
|
Build a GenBank Entrez Query
|
|
|
|
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::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::Taxonomy
|
Access to a taxonomy database
|
|
|
|
Bio::DB::Taxonomy::entrez
|
Taxonomy Entrez driver
|
|
|
|
Bio::DB::Taxonomy::flatfile
|
An implementation of Bio::DB::Taxonomy which uses local flat files
|
|
|
|
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::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::Event::EventGeneratorI
|
This interface describes the basic event generator class.
|
|
|
|
Bio::Event::EventHandlerI
|
An Event Handler Interface
|
|
|
|
Bio::Expression::FeatureGroup
|
a set of DNA/RNA features. ISA Bio::Expression::FeatureI
|
|
|
|
Bio::Expression::FeatureGroup::FeatureGroupMas50
|
|
|
|
|
Bio::Expression::FeatureI
|
an interface class for DNA/RNA features
|
|
|
|
Bio::Expression::FeatureSet::FeatureSetMas50
|
|
|
|
|
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::HitFactoryI
|
Interface for an object that builds Bio::Search::Hit::HitI objects
|
|
|
|
Bio::Factory::LocationFactoryI
|
DESCRIPTION of Interface
|
|
|
|
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::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::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::Graphics
|
Generate GD images of Bio::Seq objects
|
UNAUTHORIZED |
|
|
Bio::Graphics::ConfiguratorI
|
A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation inform
|
|
|
|
Bio::Graphics::Feature
|
A simple feature object for use with Bio::Graphics::Panel
|
UNAUTHORIZED |
|
|
Bio::Graphics::FeatureFile
|
A set of Bio::Graphics features, stored in a file
|
UNAUTHORIZED |
|
|
Bio::Graphics::FeatureFile::Iterator
|
Iterator across a Bio::Graphics::FeatureFile
|
|
|
|
Bio::Graphics::Glyph
|
Base class for Bio::Graphics::Glyph objects
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::Factory
|
Factory for Bio::Graphics::Glyph objects
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::alignment
|
The "alignment" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::anchored_arrow
|
The "anchored_arrow" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::arrow
|
The "ruler_arrow" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::box
|
The "box" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::cds
|
The "cds" glyph
|
|
|
|
Bio::Graphics::Glyph::crossbox
|
The "crossbox" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::diamond
|
The "diamond" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::dna
|
The "dna" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::dot
|
The "dot" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::ellipse
|
The "ellipse" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::ex
|
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::extending_arrow
|
The "extending arrow" glyph
|
|
|
|
Bio::Graphics::Glyph::generic
|
The "generic" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::graded_segments
|
The "graded_segments" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::group
|
The "group" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::heterogeneous_segments
|
The "heterogeneous_segments" glyph
|
|
|
|
Bio::Graphics::Glyph::line
|
The "line" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::minmax
|
The minmax glyph
|
|
|
|
Bio::Graphics::Glyph::oval
|
The "oval" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::pinsertion
|
The "Drosophila P-element Insertion" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::primers
|
The "STS primers" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::processed_transcript
|
The sequence ontology transcript glyph
|
|
|
|
Bio::Graphics::Glyph::redgreen_box
|
The "redgreen_box" glyph
|
|
|
|
Bio::Graphics::Glyph::redgreen_segment
|
|
|
|
|
Bio::Graphics::Glyph::rndrect
|
The "round rect" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::ruler_arrow
|
|
|
|
|
Bio::Graphics::Glyph::segmented_keyglyph
|
The "segmented_keyglyph" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::segments
|
The "segments" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::span
|
The "span" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::splice_site
|
The "splice_site" glyph
|
|
|
|
Bio::Graphics::Glyph::toomany
|
The "too many to show" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::track
|
The "track" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::transcript
|
The "transcript" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::transcript2
|
The "transcript2" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::translation
|
The "6-frame translation" glyph
|
|
|
|
Bio::Graphics::Glyph::triangle
|
The "triangle" glyph
|
UNAUTHORIZED |
|
|
Bio::Graphics::Glyph::xyplot
|
The xyplot glyph
|
|
|
|
Bio::Graphics::Panel
|
Generate GD images of Bio::Seq objects
|
UNAUTHORIZED |
|
|
Bio::Graphics::Pictogram
|
|
|
|
|
Bio::Graphics::RendererI
|
A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
|
|
|
|
Bio::Graphics::Util
|
|
|
|
|
Bio::IdCollectionI
|
|
|
|
|
Bio::IdentifiableI
|
interface for objects with identifiers
|
|
|
|
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::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
|
|
|
|
|
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::Matrix::Generic
|
|
|
|
|
Bio::Matrix::IO
|
A factory for Matrix parsing
|
|
|
|
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::PSM::IO
|
PSM parser
|
|
|
|
Bio::Matrix::PSM::IO::mast
|
PSM mast parser implementation
|
|
|
|
Bio::Matrix::PSM::IO::meme
|
|
|
|
|
Bio::Matrix::PSM::IO::transfac
|
|
|
|
|
Bio::Matrix::PSM::InstanceSite
|
A PSM site occurance
|
|
|
|
Bio::Matrix::PSM::InstanceSiteI
|
InstanceSite interface, holds an instance of a PSM
|
|
|
|
Bio::Matrix::PSM::Psm
|
handle combination of site matricies
|
|
|
|
Bio::Matrix::PSM::PsmHeader
|
PSM mast parser implementation
|
|
|
|
Bio::Matrix::PSM::PsmHeaderI
|
|
|
|
|
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)
|
|
|
|
Bio::Matrix::PSM::SiteMatrixI
|
SiteMatrix interface, holds a position scoring matrix (or position weight matrix)
|
|
|
|
Bio::Matrix::PhylipDist
|
A Phylip Distance Matrix object
|
|
|
|
Bio::Matrix::Scoring
|
Object which can hold scoring matrix information
|
|
|
|
Bio::Ontology::GOterm
|
representation of GO terms
|
|
|
|
Bio::Ontology::InterProTerm
|
Implementation of InterProI term interface
|
|
|
|
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
|
a Ontology Engine for GO implementing OntologyEngineI
|
|
|
|
Bio::Ontology::SimpleOntologyEngine
|
Implementation of OntologyEngineI interface
|
|
|
|
Bio::Ontology::Term
|
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::BaseSAXHandler
|
|
|
|
|
Bio::OntologyIO::Handlers::InterProHandler
|
XML handler class for InterProParser
|
|
|
|
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
|
|
|
|
|
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::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::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::Term
|
A MeSH term
|
|
|
|
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::PopGen::Genotype
|
An implementation of a genotype which is 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::csv
|
Extract individual allele data from a CSV parser
|
|
|
|
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::PrimarySeq
|
Bioperl lightweight Sequence Object
|
|
|
|
Bio::PrimarySeqI
|
[Developers] - Interface definition for a Bio::PrimarySeq
|
|
|
|
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::withrefm
|
withrefm enzyme set
|
|
|
|
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::Storable
|
object serialisation methods
|
|
|
|
Bio::Root::Utilities
|
General-purpose utility module
|
|
|
|
Bio::Root::Vector
|
Interface for managing linked lists of Perl5 objects.
|
|
|
|
Bio::Root::Version
|
provide global, distribution-level versioning
|
|
1.4 |
|
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::FastaHSP
|
HSP object for FASTA specific data
|
|
|
|
Bio::Search::HSP::GenericHSP
|
A "Generic" implementation of a High Scoring Pair
|
|
|
|
Bio::Search::HSP::HMMERHSP
|
A HSP object for HMMER results
|
|
|
|
Bio::Search::HSP::HSPFactory
|
A factory to create Bio::Search::HSP::HSPI objects
|
|
|
|
Bio::Search::HSP::HSPI
|
Interface for a High Scoring Pair in a similarity search result
|
|
|
|
Bio::Search::HSP::PSLHSP
|
A HSP for PSL output
|
|
|
|
Bio::Search::HSP::PsiBlastHSP
|
Bioperl BLAST High-Scoring Pair object
|
|
|
|
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::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::PsiBlastHit
|
Bioperl BLAST Hit 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::BlastResult
|
Blast-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::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::SearchUtils
|
Utility functions for Bio::Search:: 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::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::BSMLResultWriter
|
DESCRIPTION of Object
|
|
|
|
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
|
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::Writer::TextResultWriter
|
Object to implement writing a Bio::Search::ResultI in Text.
|
|
|
|
Bio::SearchIO::axt
|
a parser for axt format reports
|
|
|
|
Bio::SearchIO::blast
|
Event generator for event based parsing of blast reports
|
|
|
|
Bio::SearchIO::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::exonerate
|
parser for Exonerate
|
|
|
|
Bio::SearchIO::fasta
|
A SearchIO parser for FASTA results
|
|
|
|
Bio::SearchIO::hmmer
|
A parser for HMMER output (hmmpfam, hmmsearch)
|
|
|
|
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::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::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::Meta
|
|
|
|
|
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 representation of a sequence and two primers flanking a target region for amplification
|
|
|
|
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
|
interface for sequences from rich data sources, mostly databases
|
|
|
|
Bio::Seq::SeqBuilder
|
Configurable object builder for sequence stream parsers
|
|
|
|
Bio::Seq::SeqFactory
|
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
|
|
|
|
Bio::Seq::SeqFastaSpeedFactory
|
|
|
|
|
Bio::Seq::SeqWithQuality
|
Bioperl object packaging a sequence with its quality
|
|
|
|
Bio::Seq::SequenceTrace
|
Bioperl object packaging a sequence with its trace
|
|
|
|
Bio::Seq::TraceI
|
Interface definition for a Bio::Seq::Trace
|
|
|
|
Bio::SeqAnalysisParserI
|
Sequence analysis output parser interface
|
|
|
|
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
|
|
|
|
|
Bio::SeqFeature::Gene::Intron
|
DESCRIPTION of Object
|
|
|
|
Bio::SeqFeature::Gene::NC_Feature
|
DESCRIPTION of Object
|
|
|
|
Bio::SeqFeature::Gene::Poly_A_site
|
|
|
|
|
Bio::SeqFeature::Gene::Promoter
|
Describes a promotor
|
|
|
|
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::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::Tools::TypeMapper
|
maps $seq_feature->primary_tag
|
|
|
|
Bio::SeqFeature::Tools::Unflattener
|
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
|
|
|
|
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::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::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::chadoxml
|
chadoxml sequence input/output stream
|
|
|
|
Bio::SeqIO::ctf
|
ctf trace sequence input/output stream
|
|
|
|
Bio::SeqIO::embl
|
EMBL sequence input/output stream
|
|
|
|
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::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::gcg
|
GCG sequence input/output stream
|
|
|
|
Bio::SeqIO::genbank
|
|
|
|
|
Bio::SeqIO::kegg
|
KEGG sequence input/output stream
|
|
|
|
Bio::SeqIO::largefasta
|
method i/o on very large fasta sequence files
|
|
|
|
Bio::SeqIO::locuslink
|
DESCRIPTION of Object
|
|
|
|
Bio::SeqIO::metafasta
|
metafasta 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
|
|
|
|
|
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::SeqIO::tab
|
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
|
|
|
|
Bio::SeqIO::tigr
|
TIGR XML sequence input/output stream
|
|
|
|
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
|
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::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::Analysis::DNA::ESEfinder
|
a wrapper around ESEfinder server
|
|
|
|
Bio::Tools::Analysis::Protein::Domcut
|
a wrapper around Domcut server
|
|
|
|
Bio::Tools::Analysis::Protein::ELM
|
|
|
|
|
Bio::Tools::Analysis::Protein::GOR4
|
a wrapper around GOR4 protein secondary structure prediction server
|
|
|
|
Bio::Tools::Analysis::Protein::HNN
|
a wrapper around 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 Sopma protein secondary structure prediction server
|
|
|
|
Bio::Tools::Analysis::SimpleAnalysisBase
|
abstact superclass for SimpleAnalysis implementations
|
|
|
|
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
|
Lightweight BLAST parser for (iterated) psiblast reports
|
|
|
|
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::Blat
|
|
|
|
|
Bio::Tools::CodonTable
|
Bioperl codon table object
|
|
|
|
Bio::Tools::Coil
|
|
|
|
|
Bio::Tools::ECnumber
|
representation of EC numbers
|
|
|
|
Bio::Tools::EMBOSS::Palindrome
|
parse EMBOSS palindrome output
|
|
|
|
Bio::Tools::EPCR
|
Parse ePCR output and make features
|
|
|
|
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::FootPrinter
|
DESCRIPTION of Object
|
|
|
|
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
|
A parser for GLIMMER 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
|
|
|
|
|
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::Phylo::Molphy
|
DESCRIPTION of Object
|
|
|
|
Bio::Tools::Phylo::Molphy::Result
|
DESCRIPTION of Object
|
|
|
|
Bio::Tools::Phylo::PAML
|
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
|
|
|
|
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
|
DESCRIPTION of Object
|
|
|
|
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
|
UNAUTHORIZED |
|
|
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
|
DESCRIPTION of Object
|
|
|
|
Bio::Tools::PrositeScan
|
Parser for ps_scan result
|
|
|
|
Bio::Tools::Pseudowise
|
Results of one Pseudowise run
|
|
|
|
Bio::Tools::QRNA
|
A Parser for qrna output
|
|
|
|
Bio::Tools::RandomDistFunctions
|
A set of routines useful for generating random data in different distributions
|
|
|
|
Bio::Tools::RepeatMasker
|
DESCRIPTION of Object
|
|
|
|
Bio::Tools::RestrictionEnzyme
|
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
|
|
|
|
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.
|
|
|
|
Bio::Tools::Run::WrapperBase
|
A Base object for wrappers around executables
|
|
|
|
Bio::Tools::Seg
|
parse Seg output (filter low complexity protein sequence)
|
|
|
|
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::SiRNA
|
Perl object for designing small inhibitory RNAs.
|
|
|
|
Bio::Tools::Sigcleave
|
Bioperl object for sigcleave analysis
|
|
|
|
Bio::Tools::Signalp
|
|
|
|
|
Bio::Tools::Sim4::Exon
|
A single exon determined by an alignment
|
|
|
|
Bio::Tools::Sim4::Results
|
Results of one Sim4 run
|
|
|
|
Bio::Tools::Tmhmm
|
parse TmHMM output (transmembrane HMM)
|
|
|
|
Bio::Tools::WWW
|
Bioperl manager for web resources related to biology.
|
|
|
|
Bio::Tools::dpAlign
|
Perl extension to do pairwise dynamic programming sequence alignment
|
|
0.50 |
|
Bio::Tools::pICalculator
|
|
|
|
|
Bio::Tools::pSW
|
pairwise Smith Waterman object
|
|
|
|
Bio::Tree::AlleleNode
|
A Node with Alleles attached
|
|
|
|
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 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::lintree
|
Parser for lintree output trees
|
|
|
|
Bio::TreeIO::newick
|
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
|
|
|
|
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::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
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Sequence change class for polypeptides
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Bio::Variation::AAReverseMutate
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point mutation and codon information from single amino acid changes
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Bio::Variation::Allele
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Sequence object with allele-specific attributes
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Bio::Variation::DNAMutation
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DNA level mutation class
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Bio::Variation::IO
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Handler for sequence variation IO Formats
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Bio::Variation::IO::flat
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flat file sequence variation input/output stream
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Bio::Variation::IO::xml
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XML sequence variation input/output stream
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Bio::Variation::RNAChange
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Sequence change class for RNA level
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Bio::Variation::SNP
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submitted SNP
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Bio::Variation::SeqDiff
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Container class for mutation/variant descriptions
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Bio::Variation::VariantI
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Sequence Change SeqFeature abstract class
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Bio::WebAgent
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A base class for Web (any protocol) access
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Error
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Error/exception handling in an OO-ish way
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UNAUTHORIZED |
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TestInterface
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A simple subclass of Interface
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TestObject
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An implementation of TestInterface
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