Documentation
extracts BioPerl documentation and indexes it in a database for easy retrieval
check modules and scripts for authors not in AUTHORS file
check NAME in module POD has fully qualified object name
validate URLs located in module code and POD
information about modules in BioPerl core
check the POD documentation syntax in modules and scripts
install script to create symbolic links
amino acid composition of protein sequences
bioperl client for accessing and querying a bibliographic repository.
Caching BioFetch-compatible web proxy for GenBank
index sequence files using Bio::DB::Flat
sequence retrieval using OBDA registry
builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
Bulk-load a Bio::DB::GFF database from GFF files.
a chaos plot from DNA and RNA sequences
classify BLAST hits by taxonomic kingdom
Render a SearchIO parser report into a simple overview graphic
script to split an input set of database(s) into smaller pieces
Render a Genbank/EMBL sequence file graphically as a png image
extract the corresponding sequence for a specified feature type
Fast-load a Bio::DB::GFF database from GFF files.
turn FASTA -m 9 output into NCBI -m 9 tabular output
Render a Bio::Graphics Feature File
fetches sequences from bioperl indexed databases
filters searchio results, outputting a tab delimited summary
finding flanking sequences for a variant in a sequence position
Render a Bio::Graphics Feature File on the web
GC content of nucleotide sequences
Load a Bio::DB::GFF database from GENBANK files.
Genbank-gtgbrowse-friendly GFF3
Generate a histogram of Bio::DB::GFF features
First demo of Bio::Graphics glyphs
Second demo of Bio::Graphics glyphs
a test for distinguishing between selection and population expansion.
turn HMMER output into tabular format
indexes files for use by bp_fetch.pl
Load a Bio::DB::GFF database from GFF files.
query a local TaxonomyDB for species or taxonid
Convert an input mRNA/cDNA sequence into protein
mask sequence(s) based on its alignment results
Get/set Bio::DB::GFF meta-data
implement a transformer of alignments from protein to mrna coordinates
randomly mutagenize a single protein or DNA sequence
convert nexus format trees (from PAUP* and MrBayes) to new hampshire
a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
oligo count and frequency
script to calculate pairwise Ka,Ks for a set of sequences
parse single/multiple HMMSEARCH results file(s) with different output options
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
Massage WormBase GFF files into a version suitable for the Generic Genome Browser
query Entrez taxonomy database and print out information
script for submitting jobs to a remote blast server (ncbi blast queue at this time)
Turn SearchIO parseable reports(s) into a BSML report
Turn SearchIO parseable reports(s) into a set of aligned blocks
Turn SearchIO parseable reports(s) into a GFF report
turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
Turn SearchIO parseable reports(s) into TRIBE matrix
Render a SearchIO parser report into a simple overview graphic
lists the number of bases and number of sequences in specified sequence database files
generic BioPerl sequence format converter
bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
splits a sequence into equal sized chunks with an optional overlapping range
convert sequence formats
Building a taxonomic tree based on the full lineages of a set of species names
translates a sequence
convert Bio::TreeIO parseable format trees to pagel format
unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
Modules
An interface for describing sequence alignments.
Calculate some statistics for a DNA alignment
Base statistic object for Pairwise Alignments
Calculate Protein Alignment statistics (mostly distances)
Calculate some statistics for an alignment
A collection of utilities regarding converting and manipulating alignment objects
Handler for AlignIO Formats
bl2seq sequence input/output stream
clustalw sequence input/output stream
Parse EMBOSS alignment output (from applications water and needle)
fasta MSA Sequence input/output stream
Largemultifasta MSA Sequence input/output stream
Multipla Alignment Format sequence input stream
mase sequence input/output stream
Parse and Create MEGA format data files
meme sequence input/output stream
Metafasta MSA Sequence input/output stream
msf sequence input/output stream
NEXUS format sequence input/output stream
pfam sequence input/output stream
PHYLIP format sequence input/output stream
po MSA Sequence input/output stream
prodom sequence input/output stream
Read/Write PSI-BLAST profile alignment files
selex sequence input/output stream
stockholm sequence input/output stream
An interface to any (local or remote) analysis tool
Generic analysis output parser interface
Interface for analysis result objects
the base interface an annotatable object must implement
Instantiates a new Bio::AnnotationI (or derived class) through a factory
Default Perl implementation of AnnotationCollectionI
A comment object, holding text
untyped links between databases
An ontology term adapted to AnnotationI
Specialised DBLink object for Literature References
A simple scalar
A scalar with embedded structured information
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Manages types for annotation collections
Interface for annotation collections
Annotation interface
Perl module to hold and manipulate sequence assembly contigs.
Perform analysis on sequence assembly contigs.
Handler for Assembly::IO Formats
module to load phrap ACE files.
driver to load phrap.out files.
Perl module to hold and manipulate sequence assembly data.
Abstract Inteface of Sequence Assemblies
Perl module to hold and manipulate singlets from sequence assembly contigs.
A Bibliographic Query Service module
Representation of a general article
An abstract base for other biblio classes
Representation of a book
Representation of a book article
Handling the bibliographic references
A converter of a raw hash to MEDLINE citations
A converter of XML files with MEDLINE citations
A converter of a raw hash to PUBMED citations
A converter of XML files with PUBMED citations
Representation of a journal
Representation of a journal article
Representation of a MEDLINE article
Representation of a MEDLINE book
Representation of a MEDLINE book article
Representation of a MEDLINE journal
Representation of a MEDLINE journal article
Representation of an organisation
Representation of a patent
Representation of a person
Representation of a conference proceeding
Representation of a general provider
Representation of a PUBMED article
Representation of a PUBMED book article
Representation of a PUBMED journal article
Representation of a bibliographic reference
Representation of a provider of type service
Representation of a technical report
Representation of thesis
Representation of a web resource
Instantiates a new Bio::ClusterI (or derived class) through a factory
Family Interface
Sequence Family object
UniGene object
abstract interface of UniGene object
Cluster Interface
Handler for Cluster Formats
dbSNP input stream
UniGene input stream
for reading and writing codon usage tables to file
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Mapping locations through a chain of coordinate mappers
Noncontinuous match between two coordinate sets
Continuous match between two coordinate sets
transformations between gene related coordinate systems
Finds shortest path between nodes in a graph
Interface describing coordinate mappers
Continuous match between two coordinate sets
Results from coordinate transformation
Another name for Bio::Location::Simple
Another name for Bio::Location::Simple
Interface to identify coordinate mapper results
Additional methods to create Bio::Coordinate objects
Database object interface to ACeDB servers
A BioFetch-based access to a bibliographic citation retrieval
Access to PubMed's bibliographic query service
Fetch PDF for a PubMed ID
A SOAP-based access to a bibliographic query service
An interface to a Bibliographic Query Service
Database object interface to BioFetch retrieval
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Database object for retrieving using the dbfetch script
Database object interface for EMBL entry retrieval
interface for handling web queries and data retrieval from NCBI's Entrez Utilities.
simple object to hold NCBI cookie information and descriptions
retrieval of records from a list of IDs or the user's environment.
counts for a global query of Entrez databases
NCBI database information
check for and retrieve external or related ID's from a list of one or more primary ID's, including relevancy scores.
posting IDs on the remote NCBI server for batch retrieval and chained queries
Base interface class for handling web queries and data retrieval from Entrez Utilities from NCBI. You shouldn't use this class directly.
retrieval of NCBI DocSum data from a list of primary IDs or a Cookie
Database object interface to Entrez Gene
DESCRIPTION of Object
*** DESCRIPTION of Class
A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
Fast indexed access to a directory of fasta files
In file cache for BioSeq objects
Interface for indexed flat files
Interface for BioHackathon standard BDB-indexed flat file
embl adaptor for Open-bio standard BDB-indexed flat file
fasta adaptor for Open-bio standard BDB-indexed flat file
genbank adaptor for Open-bio standard BDB-indexed flat file
swissprot adaptor for Open-bio standard BDB-indexed flat file
swissprot adaptor for Open-bio standard BDB-indexed flat file
BinarySearch search indexing system for sequence files
Database object interface to GDB HTTP query
Storage and retrieval of sequence annotation data
ace interface (for multiple inheritance)
Bio::DB::GFF database adaptor for in-memory databases
iterator for Bio::DB::GFF::Adaptor::berkeleydb
Cache BioFetch objects in a Bio::DB::GFF database
Cache BioFetch objects in a Bio::DB::GFF database
Database adaptor for DBI (SQL) databases
Cache for database handles
iterator for Bio::DB::GFF::Adaptor::dbi
Database adaptor for a specific mysql schema
Unholy union between mysql GFF database and acedb database
Database adaptor for an integraded CMap/GBrowse mysql schema
Deprecated database adaptor
Database adaptor for a specific oracle schema
Unholy union between oracle GFF database and acedb database
Database adaptor for a specific postgres schema
Database adaptor for a specific postgres schema with a TSearch2 implementation
Bio::DB::GFF database adaptor for in-memory databases
iterator for Bio::DB::GFF::Adaptor::memory
Aggregate GFF groups into composite features
Alignment aggregator
Clone aggregator
The Coding Region Aggregator
Match aggregator
No aggregation
Sequence Ontology Transcript
Sequence Ontology Transcript
Transcript aggregator
UCSC acembly aggregator
UCSC ensGene aggregator
UCSC genscan aggregator
UCSC refGene aggregator
UCSC sanger22 aggregator
UCSC sanger22pseudo aggregator
UCSC softberry aggregator
UCSC twinscan aggregator
UCSC UniGene aggregator
The name of a feature
A relative segment identified by a feature type
A segment of DNA that is homologous to another
Sequence segment with relative coordinate support
Simple DNA segment object
The name of a feature type
binning utility for Bio::DB::GFF index
rearrange utility
Database object interface to GenBank
Database object interface to GenPept
abstract interface for parameter-based remote database access
Abstract interface for a sequence database
A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
Term retrieval from a Web MeSH database
A collection of routines useful for queries to NCBI databases.
Build a GenBank Entrez Query
Helper class for web-based sequence queryies
Object Interface to queryable sequence databases
Abstract interface for a sequence database
Database object interface for RefSeq retrieval
A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
Access to the Open Bio Database Access registry scheme
Normalized feature for use with Bio::DB::SeqFeature::Store
Normalized feature for use with Bio::DB::SeqFeature::Store
Interface for normalized features
Interface for normalized features whose hierarchy is stored in a table
Location-based access to genome annotation data
Storage and retrieval of sequence annotation data
Mysql implementation of Bio::DB::SeqFeature::Store
GFF3 file loader for Bio::DB::SeqFeature::Store
fetch and store objects from a BerkeleyDB
Storage and retrieval of sequence annotation data in Berkeleydb files
In-memory implementation of Bio::DB::SeqFeature::Store
Database object interface to SeqHound
Abstract Interface for Sequence databases
front end to querying databases for identifier versions
interface to NCBI Sequence Revision History page
Database object interface to SwissProt retrieval
Access to a taxonomy database
Taxonomy Entrez driver
An implementation of Bio::DB::Taxonomy which uses local flat files
An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
Artificial database that delegates to specific databases
An interface for writing to a database of sequences.
Object Interface to generalize Web Databases for retrieving sequences
Database object interface for XEMBL entry retrieval
SOAP service definition for XEMBL
Abstract interface for any object wanting to use database cross references
Simple interface to Sequence Ontology feature types
DAS-style access to a feature database
DAS-style access to a feature database
interface for objects with human readable names and descriptions
This interface describes the basic event generator class.
An Event Handler Interface
DESCRIPTION of Object
DESCRIPTION of Object
a set of DNA/RNA features. ISA Bio::Expression::FeatureI
an interface class for DNA/RNA features
DESCRIPTION of Object
an interface class for DNA/RNA probes
DESCRIPTION of Object
An interface to analysis tool factory
Interface class for Application Factories
Base class for factory classes loading drivers
A FeatureTable Location Parser
Interface for an object that builds Bio::Search::Hit::HitI objects
A factory interface for generating locations from a string
A Factory for getting markers
Interface for an object builder
Instantiates a new Bio::Root::RootI (or derived class) through a factory
A General object creator factory
Interface for an object that builds Bio::Search::Result::ResultI objects
class capable of creating SeqAnalysisParserI compliant parsers
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Interface for chained sequence processing algorithms
Interface describing the basics of a Sequence Stream.
Factory Interface for getting and writing trees from/to a data stream
the base interface an object with features must implement
Handler for FeatureIO
write features from UCSC BED format
read/write GFF feature files
read write features in GTF format
read features from InterPro XML
read/write features in PTT format
encapsulation of an interaction between 2 Bio::Seq objects
Class for reading /writing biological graph data.
class for parsing interaction data in dip format
access and manipulate PSI XML graphs
a representation of a protein interaction graph.
create and manipulate undirected graphs
graph traversal operations for Bio::Graph::SimpleGraph and Bio::Graph::Protein::Graph objects
Generate GD images of Bio::Seq objects
A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-gtvalue semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse).
A simple feature object for use with Bio::Graphics::Panel
Base class for Bio::Graphics::Feature
A set of Bio::Graphics features, stored in a file
Iterator across a Bio::Graphics::FeatureFile
Base class for Bio::Graphics::Glyph objects
Factory for Bio::Graphics::Glyph objects
The "alignment" glyph
The "anchored_arrow" glyph
the "arrow" glyph
The "box" glyph
The "broken line" glyph
The "cds" glyph
The "christmas arrow" glyph
The "crossbox" glyph
The "dashed line" glyph
The "diamond" glyph
The "dna" glyph
The "dot" glyph
A glyph that draws a "dumbbell" with the same shapes on both ends.
The "ellipse" glyph
the "ex", or "crossed box" glyph
The "extending arrow" glyph
the "flag" glyph
A GFF3-compatible gene glyph
The "generic" glyph
The "graded_segments" glyph
The "group" glyph
The "heterogeneous_segments" glyph
A glyph that draws photographs & other images
The "lightning" glyph
The "line" glyph
a base class which suppors semantic zooming of scored alignment features
The "merged_alignment" glyph
The minmax glyph
The "oval" glyph
The "pentagram" glyph
The "Drosophila P-element Insertion" glyph
The "STS primers" glyph
The sequence ontology transcript glyph
The "protein" glyph
The "ragged ends" glyph
The "redgreen_box" glyph
The "redgreen_segments" glyph
A glyph that draws the same shape repeatedly.
The "round rect" glyph
glyph for drawing an arrow as ruler (5' and 3' are marked as label)
The "saw teeth" glyph
The "segmented_keyglyph" glyph
The "segments" glyph
The sequence ontology transcript glyph
The "span" glyph
The "splice_site" glyph
The "text in box" glyph
DAS-compatible package to use for drawing a line of groups of three letters
The "tic-tac-toe" glyph
The "too many to show" glyph
The "track" glyph
The "transcript" glyph
The "transcript2" glyph
The "6-frame translation" glyph
The "triangle" glyph
The "two bolts" glyph
The "wave" glyph
The "weighted arrow" glyph
The whiskerplot glyph
The xyplot glyph
Generate GD images of Bio::Seq objects
generate SVG output of Pictogram display for consensus motifs
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.
non-object-oriented utilities used in Bio::Graphics modules
interface for objects with multiple identifiers
interface for objects with identifiers
Abstract interface for indexing a flat file
base class for AbstractSeq
Indexes Blast reports and supports retrieval based on query accession(s)
Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
Interface for indexing (multiple) fasta files
Interface for indexing (multiple) fastq files
Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
Interface for indexing (multiple) fasta qual files
Interface for indexing swisspfam files
Interface for indexing one or more Swissprot files.
AARange abstract class for LiveSeq
DoubleChain DataStructure for Perl
Double linked chain data structure
DNA object for LiveSeq
Range abstract class for LiveSeq
Range abstract class for LiveSeq
Loader for LiveSeq from EMBL entries with BioPerl
Parent Loader for LiveSeq
Range abstract class for LiveSeq
Mutation event descriptor class
Package mutating LiveSequences
Prim_Transcript class for LiveSeq
Range abstract class for LiveSeq
Repeat_Region class for LiveSeq
Repeat_Unit class for LiveSeq
Abstract sequence interface class for LiveSeq
Transcript class for LiveSeq
Translation class for LiveSeq
A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
Implementation of a Atomic Location on a Sequence
class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Implementation of a Location on a Sequence which has unclear start and/or end locations
Abstract interface of a Location on a Sequence which has unclear start/end location
class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Implementation of a Simple Location on a Sequence
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Abstract interface of a Location on a Sequence
An central map object representing a clone
A MapI implementation handling the contigs of a Physical Map (such as FPC)
A Bio::MapI compliant map implementation handling cytogenic bands
An object representing a marker.
Marker class with cytogenetic band storing attributes
An Entity Interface
An central map object representing a marker
A representation of a genetic linkage map.
Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
Interface for describing Map objects in bioperl
An object representing a generic map element that can have multiple locations in several maps.
An object that can be placed in a map
An central map object representing a generic marker that can have multiple location in several maps.
Interface for basic marker functionality
An object representing a Microsatellite marker.
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.
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.
A class for handling a Physical Map (such as FPC)
A single position of a Marker, or the range over which that marker lies, in a Map
A Position Handler Implementation
A Position Handler Interface
Abstracts the notion of a position having a value in the context of a marker and a Map
Represents what a Position's coordiantes are relative to.
Interface for describing what a Position's coordiantes are relative to.
A MapI implementation handling the basics of a Map
A Map Factory object
A FPC Map reader
A Mapmaker Map reader
A generic matrix implementation
A factory for Matrix parsing
A parser for PHYLIP distance matricies
A parser for PAM/BLOSUM matricies
An interface for describing a Matrix
PSM parser
PSM mast parser implementation
motif fasta format parser
PSM meme parser implementation
PSM psiblast parser
PSM transfac parser
A PSM site occurance
InstanceSite interface, holds an instance of a PSM
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
handle combination of site matricies
handle combination of site matricies
PSM mast parser implementation
abstract interface to handler of site matricies
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
A Phylip Distance Matrix object
Object which can hold scoring matrix information
Keep track of where to find ontologies. Allows lookups by name.
representation of GO terms
Implementation of InterProI term interface
An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
representation of OBO terms
standard implementation of an Ontology
Interface a minimal Ontology implementation should satisfy
Interface for an ontology implementation
A repository of ontologies
a path for an ontology term graph
Interface for a path between ontology terms
a relationship for an ontology
Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Interface for a relationship between ontology terms
a relationship type for an ontology
a Ontology Engine for GO implementing OntologyEngineI
Graph adaptor for Bio::Ontology::SimpleGOEngine
Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine
Implementation of OntologyEngineI interface
implementation of the interface for ontology terms
Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
interface for ontology terms
Parser factory for Ontology formats
XML handler class for InterProParser
parse an InterPro XML file and persist the resulting terms to a Biosql database
Parser for InterPro xml files.
a base class parser for GO flat-file type formats
a parser for the Gene Ontology flat-file format
a parser for OBO flat-file format from Gene Ontology Consortium
a base class parser for simple hierarchy-by-indentation type formats
a parser for the Sequence Ontology flat-file format
Functional access to BioPerl for people who don't know objects
Representation of a correlating phenotype in a given species
A MeSH term
Context for a MeSH term
Representation of context/value(-range)/unit triplets
Representation of a Mini MIM entry
represents OMIM (Online Mendelian Inheritance in Man) database entries
Representation of a allelic variant of the OMIM database
parser for the OMIM database
A class for modeling phenotypes
An interface for classes modeling phenotypes
An implementation of GenotypeI which is just an allele container
A marker and alleles for a specific individual
Input individual,marker,allele information
A parser for HapMap output data
A parser for Phase format data
Extract individual allele data from PrettyBase format
An implementation of an Individual who has Genotype or Sequence Results
An individual who has Genotype or Sequence Results
A genetic marker which one uses to generate genotypes
A Population Genetic conceptual marker
A collection of methods for calculating statistics about a population or sets of populations
A population of individuals
Interface for Populations
A Coalescent simulation factory
A simple genetic drift simulation
Population Genetics statistical tests
Haplotype tag object.
Utilities for working with PopGen data and objects
Bioperl lightweight Sequence Object
Interface definition for a Bio::PrimarySeq
A base module for fast 'pull' parsing
Pure perl RangeI implementation
Range interface
cutting sequences with restriction enzymes
A single restriction endonuclease (cuts DNA at specific locations)
A single restriction endonuclease
A single restriction endonuclease
Set of restriction endonucleases
Interface class for restriction endonuclease
Handler for sequence variation IO Formats
bairoch enzyme set
base enzyme set
itype2 enzyme set
withrefm enzyme set
Generic exception objects for Bioperl
module for fallback HTTP get operations when LWP:: is unavailable
module providing several methods often needed when dealing with file IO
Hash-based implementation of Bio::Root::RootI
Abstract interface to root object code
object serialisation methods
provide global, distribution-level versioning
An object for Blast statistics
Utility functions for Bio::Search:: BLAST objects
Interface for a database used in a sequence search
Generic implementation of Bio::Search::DatabaseI
An object for statistics
Bioperl BLAST High-Scoring Pair object
HSP object for FASTA specific data
A "Generic" implementation of a High Scoring Pair
A HSP object for HMMER results
A factory to create Bio::Search::HSP::HSPI objects
Interface for a High Scoring Pair in a similarity search result
A parser and HSP object for hmmpfam hsps
A HSP for PSL output
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::HSPI interface for pull parsers.
HSP object suitable for describing WABA alignments
Blast-specific subclass of Bio::Search::Hit::GenericHit
Hit object specific for Fasta-generated hits
A generic implementation of the Bio::Search::Hit::HitI interface
A Hit module for HMMER hits
A factory to create Bio::Search::Hit::HitI objects
Interface for a hit in a similarity search result
A parser and hit object for hmmpfam hits
Bioperl BLAST Hit object
Bio::Search::Hit::HitI interface for pull parsers.
A generic implementation of the Bio::Search::Iteration::IterationI interface.
Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
DESCRIPTION of Object
Blast-specific subclass of Bio::Search::Result::GenericResult
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
A Result object for HMMER results
A parser and result object for hmmpfam results
Bio::Search::Result::ResultI interface for 'pull' parsers
A factory to create Bio::Search::Result::ResultI objects
Abstract interface to Search Result objects
Result object for WABA alignment output
Utility functions for Bio::Search:: objects
A Base object for statistics
A perl wrapper around Sean Eddy's histogram object
Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
An abstract Event Handler for Search Result parsing
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Interface for outputting parsed Search results
BSML output writer
Interface for outputting parsed search results in Gbrowse GFF format
Tab-delimited data for Bio::Search::HSP::HSPI objects
write a Bio::Search::ResultI in HTML
Tab-delimited data for Bio::Search::Hit::HitI objects
Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Object to implement writing a Bio::Search::ResultI in Text.
a parser for axt format reports
Event generator for event based parsing of blast reports
Driver module for SearchIO for parsing NCBI -m 8/9 format
A SearchIO implementation of NCBI Blast XML parsing.
parser for Exonerate
A SearchIO parser for FASTA results
A parser for HMMER output (hmmpfam, hmmsearch)
A parser for HMMER output
a driver module for Bio::SearchIO to parse megablast reports (format 0)
A parser for PSL output (UCSC)
parser for Sim4 alignments
SearchIO parser for Jim Kent WABA program alignment output
Parsing of wise output as alignments
Sequence object, with features
Base implementation for a SequenceProcessor
subtype of Bio::LocatableSeq to store DNA that encodes a protein
LocatableSeq object that stores sequence as files in the tempdir
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
SeqI compliant object that stores sequence as files in /tmp
Interface class for sequences that cache their residues in a temporary file
Generic superclass for sequence objects with residue-based meta information
array-based generic implementation of a sequence class with residue-based meta information
Interface for sequence objects with residue-based meta information
Bioperl lightweight Quality Object
A representation of a sequence and two primers flanking a target region
Interface definition for a Bio::Seq::Qual
Implementation of sequence with residue quality and trace values
Module implementing a sequence created from a rich sequence database entry
interface for sequences from rich data sources, mostly databases
Configurable object builder for sequence stream parsers
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bioperl object packaging a sequence with its quality
Bioperl object packaging a sequence with its trace
Interface definition for a Bio::Seq::Trace
Sequence analysis output parser interface
PLEASE PUT SOMETHING HERE
integrates SeqFeatureIs annotation
A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.
An interface for a collection of SeqFeatureI objects.
Computation SeqFeature
hold pair feature information e.g. blast hits
a feature representing an exon
Interface for a feature representing an exon
A feature representing an arbitrarily complex structure of a gene
A feature representing an arbitrarily complex structure of a gene
An intron feature
superclass for non-coding features
poly A feature
Describes a promoter
A feature representing a transcript
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
A feature representing an untranslated region that is part of a transcriptional unit
Generic SeqFeature
handle features when truncation/revcom sequences span a feature
Primer Generic SeqFeature
Perl object for small inhibitory RNAs.
Perl object for small inhibitory RNA (SiRNA) oligo pairs
A sequence feature based on similarity
Sequence feature based on the similarity of two sequences.
generates unique persistent names for features
maps $seq_feature-gtprimary_tag
maps $seq_feature-gtprimary_tag
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
a strongly typed SeqFeature
Abstract interface of a Sequence Feature
Handler for SeqIO Formats
Helper class for Embl/Genbank feature tables
Treating a set of files as a single input stream
abi trace sequence input/output stream
ace sequence input/output stream
AGAVE sequence output stream.
alf trace sequence input/output stream
asciitree sequence input/output stream
BSML sequence input/output stream
BSML sequence input/output stream using SAX
chadoxml sequence output stream
chaos sequence input/output stream
chaosxml sequence input/output stream
ctf trace sequence input/output stream
EMBL sequence input/output stream
Entrez Gene ASN1 parser
sequence input/output stream from a MSExcel-formatted table
exp trace sequence input/output stream
fasta sequence input/output stream
fastq sequence input/output stream
a class for parsing and writing game-XML
a class for handling feature elements
PerlSAX handler for game-XML
a base class for game-XML parsing
a class for writing game-XML
a class for handling game-XML sequences
GCG sequence input/output stream
GenBank sequence input/output stream
InterProScan XML input/output stream
KEGG sequence input/output stream
method i/o on very large fasta sequence files
Lasergene sequence file input/output stream
LocusLink input/output stream
metafasta sequence input/output stream
.phd file input/output stream
PIR sequence input/output stream
pln trace sequence input/output stream
.qual file input/output stream
raw sequence file input/output stream
.scf file input/output stream
DNA strider sequence input/output stream
Swissprot sequence input/output stream
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
sequence input/output stream from a delimited table
TIGR XML sequence input/output stream
Parse TIGR (new) XML
reading/writing sequences in NCBI TinySeq format
XML event handlers to support NCBI TinySeq XML parsing
ztr trace sequence input/output stream
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
A simple interface to any (local or remote) analysis tool
Generic species object
Bioperl structure Object, describes an Atom
Bioperl structure Object, describes a chain
Bioperl structure Object, describes the whole entry
Handler for Structure Formats
PDB input/output stream
Bioperl structure Object, describes a Model
Bioperl structure Object, describes a Residue
Module for parsing/accessing dssp output
Module for parsing/accessing stride output
Abstract Interface for a Structure objects
BSANE/BioCORBA compliant symbol list alphabet
A Symbol Alphabet
A ready made DNA alphabet
A ready made Protein alphabet
A biological symbol
Interface for a Symbol
A node in a represented taxonomy
representing Taxonomy.
interface to define how to access NCBI Taxonoy
A node in a represented taxonomy
Generic Taxonomic Entity object
An Organism Level Implementation of TreeI interface.
Base object for alignment factories
A module to work with objects from consed .ace files
A kludge to do specialized trimming of sequence based on quality.
a wrapper around ESEfinder server
a wrapper around Domcut server
a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
a wrapper around GOR4 protein secondary structure prediction server
a wrapper around the HNN protein secondary structure prediction server
a wrapper around Mitoprot server
a wrapper around NetPhos server
a wrapper around the Scansite server
a wrapper around the Sopma protein secondary structure prediction server
abstract superclass for SimpleAnalysis implementations
Base class for analysis result objects and parsers
Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Lightweight BLAST parser
Blast report High Scoring Pair (HSP)
object for parsing single iteration of a PSIBLAST report
A Blast Subject (database search Hit)
Lightweight BLAST parser for (iterated) psiblast reports
parser for Blat program
Bioperl codon table object
parser for Coil output
representation of EC numbers (Enzyme Classification)
parse EMBOSS palindrome output
Parse ePCR output and make features
a parser for ERPIN output
Results of one ESTScan run
Results of one Eponine run
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
parse results of one Fgenesh run
write sequence features in FootPrinter format
A Bio::SeqAnalysisParserI compliant GFF format parser
Calculates relative electrophoretic migration distances
Results of one geneid run
Results of one Genemark run
Results of one Genewise run
Results of one Genomewise run
Results of one Genscan run
parser for GlimmerM/GlimmerHMM eukaryotic gene predictions
Results of one Grail run
Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Perl extension to perform Hidden Markov Model calculations
One particular domain hit from HMMER
Object representing HMMER output results
Set of identical domains from HMMER matches
Parser for Hmmpfam program
Generates unique Seq objects from an ambiguous Seq object
Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Results of one MZEF run
Object holding alternative alphabet coding for one protein sequence
parser for Molphy output
container for data parsed from a ProtML run
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
A container for NSSite Model Result from PAML
A PAML result set object
parser for ProtDist output
A predicted exon feature
a predicted gene structure feature
base class for common assessor things
interface for assessing primer pairs
position of a single primer
two primers on left and right side
Create input for and work with the output from the program primer3
Parser for FingerPRINTScanII program
parse Profile output
parser for Promoterwise tab format output
Parser for ps_scan result
Results of one Pseudowise run
A Parser for qrna output
A parser for RNAMotif output
A set of routines useful for generating random data in different distributions
a parser for RepeatMasker output
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
An object for the parameters used to run programs
A Base object for the parameters used to run programs
Object for remote execution of the NCBI Blast via HTTP
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
A Base object for wrappers around executables
parse seg output
represent a sequence pattern or motif
Object holding statistics for one particular sequence
Object holding n-mer statistics for a sequence
Perl object for designing small inhibitory RNAs.
Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
Bioperl object for sigcleave analysis
parser for Signalp output
A single exon determined by an alignment
Results of one Sim4 run
A single exon determined by an alignment
Results of a Spidey run
parse TMHMM output (TransMembrane HMM)
Perl extension to do pairwise dynamic programming sequence alignment
Parse ipcress output and make features
Parse isPcr output and make features
calculate the isoelectric point of a protein
pairwise Smith Waterman object
A parser for tRNAscan-SE output
A Node with Alleles attached
Testing compatibility of phylogenetic trees with nested taxa.
Construct a tree using distance based methods
Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
A Simple Tree Node
Interface describing a Tree Node
A Simple Tree Node with support for NHX tags
TreeFactory for generating Random Trees
Calculate certain statistics for a Tree
An Implementation of TreeI interface.
Decorated Interface implementing basic Tree exploration methods
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Parser for Tree files
Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
A TreeIO driver module for parsing Algorithm::Cluster::treecluster output
Parser for lintree output trees
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
A TreeIO driver module for parsing Nexus tree output from PAUP
TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
Bio::TreeIO driver for Pagel format
A simple output format that converts a Tree object to an SVG output
A simple output format which displays a tree as an ASCII drawing
Descendant of Bio::SeqI that allows updates
Sequence change class for polypeptides
point mutation and codon information from single amino acid changes
Sequence object with allele-specific attributes
DNA level mutation class
Handler for sequence variation IO Formats
flat file sequence variation input/output stream
XML sequence variation input/output stream
Sequence change class for RNA level
submitted SNP
Container class for mutation/variant descriptions
Sequence Change SeqFeature abstract class
A base class for Web (any protocol) access
get BioPerl method and package information from a Berkeley DB
Provides
in Bio/AnalysisI.pm
in Bio/DB/Fasta.pm
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
in Bio/DB/GFF.pm
in Bio/DB/SeqFeature/Store/berkeleydb.pm
in Bio/DB/SeqFeature/Store/memory.pm
in Bio/DB/Fasta.pm
in Bio/DB/GFF/Adaptor/berkeleydb.pm
Examples
- examples/Bio-DB-GFF/load_ucsc.pl
- examples/align/align_on_codons.pl
- examples/align/aligntutorial.pl
- examples/align/clustalw.pl
- examples/align/simplealign.pl
- examples/biblio/biblio-eutils-example.pl
- examples/biblio/biblio-soap-example.pl
- examples/biblio/biblio_soap.pl
- examples/biographics/all_glyphs.pl
- examples/biographics/dynamic_glyphs.pl
- examples/biographics/feature_data.gff
- examples/biographics/feature_data.txt
- examples/biographics/lots_of_glyphs.pl
- examples/biographics/render_sequence.pl
- examples/bioperl.pl
- examples/cluster/dbsnp.pl
- examples/contributed/nmrpdb_parse.pl
- examples/contributed/prosite2perl.pl
- examples/contributed/rebase2list.pl
- examples/db/dbfetch
- examples/db/est_tissue_query.pl
- examples/db/gb2features.pl
- examples/db/getGenBank.pl
- examples/db/get_seqs.pl
- examples/db/rfetch.pl
- examples/db/use_registry.pl
- examples/generate_random_seq.pl
- examples/liveseq/change_gene.pl
- examples/longorf.pl
- examples/make_primers.pl
- examples/popgen/parse_calc_stats.pl
- examples/rev_and_trans.pl
- examples/revcom_dir.pl
- examples/root/README
- examples/root/exceptions1.pl
- examples/root/exceptions2.pl
- examples/root/exceptions3.pl
- examples/root/exceptions4.pl
- examples/searchio/blast_example.pl
- examples/searchio/custom_writer.pl
- examples/searchio/hitwriter.pl
- examples/searchio/hspwriter.pl
- examples/searchio/htmlwriter.pl
- examples/searchio/psiblast_features.pl
- examples/searchio/psiblast_iterations.pl
- examples/searchio/rawwriter.pl
- examples/searchio/resultwriter.pl
- examples/searchio/waba2gff.pl
- examples/searchio/waba2gff3.pl
- examples/sirna/TAG
- examples/sirna/rnai_finder.cgi
- examples/structure/structure-io.pl
- examples/subsequence.cgi
- examples/tk/gsequence.pl
- examples/tk/hitdisplay.pl
- examples/tools/extract_genes.pl
- examples/tools/gb_to_gff.pl
- examples/tools/gff2ps.pl
- examples/tools/parse_codeml.pl
- examples/tools/psw.pl
- examples/tools/run_genscan.pl
- examples/tools/run_primer3.pl
- examples/tools/seq_pattern.pl
- examples/tools/standaloneblast.pl
- examples/tree/paup2phylip.pl