Changes for version 1.4

  • 1.4. Stable major release
  • Since initial 1.2.0, 3000 separate changes have been made to make this release.
    • o installable scripts
    • o global module version from Bio::Root:Version
    • o Bio::Graphics
      • major improvements; SVG support
    • o Bio::Popgen
      • population genetics
      • support several population genetics types of questions.
      • Tests for statistical neutrality of mutations (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics. Tests of population structure (Wright's F-statistic: Fst) is in Bio::PopGen::PopStats. Calculating composite linkage disequilibrium (LD) is available in Bio::PopGen::Statistics as well.
      • Bio::PopGen::IO for reading in prettybase (SeattleSNPs) and csv (comma delimited formatted) data.
      • a directory for implementing population simulations has been added Bio::PopGen::Simulation and 2 simulations - a Coalescent and a simple single-locus multi-allele genetic drift simulation have been provided. This replaces the code in Bio::Tree::RandomTree which has been deprecated until proper methods for generating random phylogenetic trees are implemented.
    • o Bio::Restriction
      • new restrion analysis modules
    • o Bio::Tools::Analysis
      • web based DNA and Protein analysis framework and several implementations
    • o Bio::Seq::Meta
      • per residue annotable sequences
    • o Bio::Matrix
      • Bio::Matrix::PSM - Position Scoring Matrix
      • Bio::Matrix::IO has been added for generalized parsing of matrix data. Matrix::IO::scoring and Matrix::IO::phylip are initial implementations for parsing BLOSUM/PAM and Phylip Distance matricies respectively. A generic matrix implementation for general use was added in Bio::Matrix::Generic.
    • o Bio::Ontology
      • major changes
    • o Bio:Tree
    • o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
      • small inhibitory RNA
    • o Bio::SeqFeature::Tools
      • seqFeature mapping tools
      • Bio::SeqFeature::Tools::Unflattener.pm
        • deal with mapping GenBank feature collections into Chado/GFF3 processable feature sets (with SO term mappings)
    • o Bio::Tools::dpAlign
      • pure perl dynamic programming sequence alignment
      • needs Bioperl-ext
    • o new Bio::SearchIO formats
    • o new Bio::SeqIO formats
      • chado, tab, kegg, tigr, game
      • axt and psl: UCSC formats.
      • blasttable: NCBI -m 8 or -m 9 format from blastall
      • important fixes for old modules
    • o Bio::AlignIO: maf
    • o improved Bio::Tools::Genewise
    • o Bio::SeqIO now can recongnize sequence formats automatically from stream
    • o new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
    • o Bio::DB::Registry bugs fixed
      • BerkeleyDB-indexed flat files can be used by the OBDA system
      • Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all used by the OBDA system
    • o several new HOWTOs
      • SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases
    • o hundreds of new and improved files
    • o o Bio::Tree::AlleleNode has been updated to be a container of an Bio::PopGen::Individual object for use in the Coalescent simulations.

Documentation

a tutorial for bioperl
check modules and scripts for authors not in AUTHORS file
information about modules in BioPerl core
check the POD documentation syntax in modules and scripts

Modules

An interface for describing sequence alignments.
Calculate some statistics for a DNA alignment
Base statistic object for Pairwise Alignments
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
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
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
DESCRIPTION of Object
An ontology term adapted to AnnotationI
Specialised DBLink object for Literature References
A scalar with embedded structured information
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
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
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
A Bio::DB::RandomAccessI compliant class which wraps a priority 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)
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
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 mysql schema
iterator for Bio::DB::GFF::Adaptor::memory
Aggregate GFF groups into composite features
The Coding Region Aggregator
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 a sequence database
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
Access to the Open Bio Database Access registry scheme
Abstract Interface for Sequence databases
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
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
a set of DNA/RNA features. ISA Bio::Expression::FeatureI
an interface class for DNA/RNA features
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
DESCRIPTION of Interface
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
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
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 "cds" glyph
The "crossbox" glyph
The "diamond" glyph
The "dna" glyph
The "dot" glyph
The "ellipse" glyph
The "crossbox" glyph
The "extending arrow" glyph
The "generic" glyph
The "graded_segments" glyph
The "group" glyph
The "heterogeneous_segments" glyph
The "line" glyph
The minmax glyph
The "oval" glyph
The "Drosophila P-element Insertion" glyph
The "STS primers" glyph
The sequence ontology transcript glyph
The "redgreen_box" glyph
The "redgreen_segments" glyph
The "round rect" glyph
The "ruler_arrow" glyph
The "segmented_keyglyph" glyph
The "segments" glyph
The "span" glyph
The "splice_site" 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 xyplot glyph
Generate GD images of Bio::Seq objects
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.
interface for objects with multiple identifiers
interface for objects with identifiers
Abstract interface for indexing a flat file
Base class for AbstractSeq s
Indexes Blast reports and supports retrieval based on query accession(s)
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Interface for indexing (multiple) fasta files
Interface for indexing (multiple) fastq files
Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format).
Interface for indexing swisspfam files
Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).
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
Loader for LiveSeq from EMBL entries with SRS
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
A Bio::MapI compliant map implementation handling cytogenic bands
An object representing a marker.
Marker class with cytogenetic band storing attributes
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 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 single position of a Marker in a Map
Abstracts the notion of a position having a value in the context of a marker and a Map
A MapI implementation handling the basics of a Map
A Map Factory object
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 mast parser implementation
PSM meme parser implementation
PSM transfac parser
A PSM site occurance
InstanceSite interface, holds an instance of a PSM
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)
SiteMatrix interface, holds a position scoring matrix (or position weight matrix)
A Phylip Distance Matrix object
Object which can hold scoring matrix information
representation of GO terms
Implementation of InterProI term interface
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
Implementation of OntologyEngineI interface
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
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 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
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 a genotype which is an allele container
A marker and alleles for a specific individual
Input individual,marker,allele information
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
Bioperl lightweight Sequence Object
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
Exception class for Perl 5 objects
Generic exception objects for Bioperl
Global variables and utility functions
module for fallback HTTP get operations when LWP:: is unavailable
module providing several methods often needed when dealing with file IO
Input and output manager for Perl5 objects.
A core Perl 5 object.
Hash-based implementation of Bio::Root::RootI
Abstract interface to root object code
object serialisation methods
General-purpose utility module
Interface for managing linked lists of Perl5 objects.
provide global, distribution-level versioning
A generic cross-reference object.
Utility functions for Bio::Search:: BLAST objects
Interface for a database used in a sequence search
Generic implementation of Bio::Search::DatabaseI
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 HSP for PSL output
Bioperl BLAST High-Scoring Pair object
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
Bioperl BLAST Hit object
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 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 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
Interface for outputting parsed search results in Gbrowse GFF format
Tab-delimited data for Bio::Search::HSP::HSPI objects
Object to implement writing 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 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
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
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 for amplification
Interface definition for a Bio::Seq::Qual
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
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
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
Describes a promotor
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.
maps $seq_feature-gtprimary_tag
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
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
alf trace sequence input/output stream
asciitree sequence input/output stream
BSML sequence input/output stream
chadoxml sequence input/output stream
ctf trace sequence input/output stream
EMBL sequence input/output stream
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
KEGG sequence input/output stream
method i/o on very large fasta sequence files
DESCRIPTION of Object
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
Swissprot sequence input/output stream
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
TIGR XML sequence input/output stream
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
DESCRIPTION of Object
A Symbol Alphabet
A ready made DNA alphabet
A ready made Protein alphabet
A biological symbol
Interface for a Symbol
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 GOR4 protein secondary structure prediction server
a wrapper around 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 Sopma protein secondary structure prediction server
abstact 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
Bioperl BLAST sequence analysis object
Bioperl BLAST High-Scoring Segment Pair object
Bioperl Utility module for HTML formatting Blast reports
Bioperl BLAST "Hit" object
Bioperl codon table object
representation of EC numbers
parse EMBOSS palindrome output
Parse ePCR output and make features
Results of one ESTScan run
Results of one Eponine run
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
DESCRIPTION of Object
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
A parser for GLIMMER 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.
One particular domain hit from HMMER
Object representing HMMER output results
Set of identical domains from HMMER matches
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
DESCRIPTION of Object
DESCRIPTION of Object
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
DESCRIPTION of Object
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
DESCRIPTION of Object
Parser for ps_scan result
Results of one Pseudowise run
A Parser for qrna output
A set of routines useful for generating random data in different distributions
DESCRIPTION of Object
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
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.
A Base object for wrappers around executables
parse Seg output (filter low complexity protein sequence)
Bioperl sequence analysis base class.
Bioperl object for a sequence pattern or motif
Object holding statistics for one particular sequence
Object holding n-mer statistics for one sequence
Perl object for designing small inhibitory RNAs.
Bioperl object for sigcleave analysis
A single exon determined by an alignment
Results of one Sim4 run
parse TmHMM output (transmembrane HMM)
Bioperl manager for web resources related to biology.
Perl extension to do pairwise dynamic programming sequence alignment
pairwise Smith Waterman object
A Node with Alleles attached
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
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.
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

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/Expression/FeatureGroup/FeatureGroupMas50.pm
in Bio/Expression/FeatureSet/FeatureSetMas50.pm
in Bio/Graphics/Util.pm
in Bio/DB/Fasta.pm

Examples