Changes for version 1.0.2
- o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided in this release will not work after December 2002 when NCBI shuts off the old Entrez cgi scripts. We have already fixed on our main development branch and the functionality will be available in the next stable bioperl release (1.2) slated for Fall 2002.
- o Numerous parsing bugs in Bio::SearchIO::fasta found through testset by Robin Emig. These were fixed as was the get_aln method in Bio::Search::HSP::GenericHSP to handle the extra context sequence that is provided with a FastA alignment.
- o Migrating differences between Bio::Search::XX::BlastXX to Bio::Search::XX::GenericXX objects. This included mechanism to retrieve whole list of HSPs from Hits and whole list of Hits from Results in addition to the current next_XX iterator methods that are available. Added seq_inds() method to GenericHSP which identifies indexes in the query or hit sequences where conserved,identical,gaps, or mismatch residues are located (adapted from Steve Chervitz's implementation in BlastHSP).
- o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release. Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
- o Bio::Graphics glyph set improved and extended for GBrowse release
- o Bio::Tree::Tree get_nodes implementation improvement thanks to Howard Ross notice performance problem when writing out unbalanced trees.
- o Bio::Location::Fuzzy::new named parameter -loc_type became -location_type, Bio::Location::Simple::new named parameter -seqid becamse -seq_id.
- o Fixed major Bio::AlignIO::emboss parsing bug on needle output, was mis-detecting that gaps should be placed at the beginning of the alignment when the best alignment starts internally in the sequence.
Documentation
Bioperl Design Documentation
Coordinated OOP-Perl Modules for Biology
a tutorial for bioperl
Massage Gadfly's GFF format into a form suitable for Bio::DB::GFF
Massage SGD's feature dump format into a form suitable for Bio::DB::GFF
generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
fetches sequences from bioperl indexed databases
indexes files for use by bpfetch
Render a Bio::Graphics Feature File
you will want to change this script
Modules
An interface for describing sequence alignments.
Handler for AlignIO Formats
bl2seq sequence input/output stream
clustalw sequence input/output stream
Parse EMBOSS alignment output (from applications water and needle)
fasta sequence input/output stream
mase sequence input/output stream
Parse and Create MEGA format data files
meme 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
Generic analysis output parser interface
Interface for analysis result objects
A generic object for annotations.
Default Perl implementation of AnnotationCollectionI
A comment object, holding text
DESCRIPTION of Object
Specialised DBLink object for Literature References
A simple scalar
Manages types for annotation collections
Interface for annotation collections
Annotation interface
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
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
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
Binary search indexing system for sequence files
Database object interface to GDB HTTP query
Storage and retrieval of sequence annotation data
Cache BioFetch objects in a Bio::DB::GFF database
Database adaptor for DBI (SQL) databases
Cache for database handles
Database adaptor for a specific mysql schema
Optimized Bio::DB::GFF adaptor for mysql
Aggregate GFF groups into composite features
Alignment aggregator
Clone aggregator
No aggregation
Transcript 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
Database object interface to GenBank
Database object interface to GenPept
Abstract interface for a sequence database
A collection of routines useful for queries to NCBI 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
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
DAS-style access to a feature database
DAS-style access to a feature database
This interface describes the basic event generator class.
An Event Handler Interface
Interface class for Application Factories
Factory for Bio::Search::Hit::BlastHit objects
Factory for Bio::Search::Result::BlastResult objects
Base class for factory classes loading drivers
EMBOSS appliaction factory class
Interface for an object that builds Bio::Search::Hit::HitI objects
A Factory for getting markers
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
Factory Interface for getting and writing trees from/to a data stream
Generate GD images of Bio::Seq objects
A simple feature object for use with Bio::Graphics::Panel
A set of Bio::Graphics features, stored in a file
Base class 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 "oval" glyph
The "Drosophila P-element Insertion" glyph
The "STS primers" glyph
The "round rect" glyph
The "ruler_arrow" glyph
The "segmented_keyglyph" glyph
The "segments" glyph
The "span" glyph
The "too many to show" glyph
The "track" glyph
The "transcript" glyph
The "transcript2" glyph
The "6-frame translation" glyph
The "triangle" glyph
Generate GD images of Bio::Seq objects
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.
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
Functional access to BioPerl for people who don't know objects
Bioperl lightweight Sequence Object
Interface definition for a Bio::PrimarySeq
Pure perl RangeI implementation
Range interface
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
General-purpose utility module
Interface for managing linked lists of Perl5 objects.
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
DESCRIPTION of Object
Interface for a High Scoring Pair in a similarity search result
Bioperl BLAST Hit object
Hit object specific for Fasta-generated hits
A generic implementation of the Bio::Search::Hit::HitI interface
Interface for a hit in a similarity search result
A top-level BLAST Report object
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
Abstract interface to Search Result 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.
Interface for outputting parsed Search results
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.
Event generator for event based parsing of blast reports
A SearchIO implementation of NCBI Blast XML parsing.
A SearchIO parser for FASTA results
Parser for traditional BLAST and PSI-BLAST reports
Sequence object, with features
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
Bioperl lightweight Quality Object
Interface definition for a Bio::Seq::Qual
Module implementing a sequence created from a rich sequence database entry
RichSeq interface, mainly for database orientated sequences
Bioperl object packaging a sequence with its quality
Sequence analysis output parser interface
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
DESCRIPTION of Object
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 transcription unit
Generic SeqFeature
A sequence feature based on similarity
Sequence feature based on the similarity of two sequences.
Abstract interface of a Sequence Feature
Abstract Interface of Sequence (with features)
Handler for SeqIO Formats
Helper class for Embl/Genbank feature tables
Treating a set of files as a single input stream
ace sequence input/output stream
BSML sequence input/output stream
EMBL sequence input/output stream
fasta sequence input/output stream
fastq sequence input/output stream
Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.
GAME helper via PerlSAX helper.
GAME helper via PerlSAX helper.
GAME helper via PerlSAX helper.
GCG sequence input/output stream
GenBank sequence input/output stream
method i/o on very large fasta sequence files
.phd file input/output stream
PIR 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
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
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
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.
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)
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
Parse ePCR output and make features
Results of one ESTScan run
A Bio::SeqAnalysisParserI compliant GFF format parser
Calculates relative electrophoretic migration distances
Results of one Genemark run
Results of one Genscan run
Results of one Grail run
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
A predicted exon feature
a predicted gene structure feature
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
class for EMBOSS Applications
Object for remote execution of the NCBI Blast via HTTP
Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq)
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
Bioperl object for sigcleave analysis
A single exon determined by an alignment
Results of one Sim4 run
Abstract state machine object
IO-based implementation of AbstractStateMachine
Bioperl manager for web resources related to biology.
pairwise Smith Waterman object
DESCRIPTION of Object
A Simple Tree Node
Interface describing a Tree Node
TreeFactory for generating Random Trees
Calculate certain statistics for a Tree
An Implementation of TreeI interface.
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
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
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
Container class for mutation/variant descriptions
Sequence Change SeqFeature abstract class
Provides
in Bio/DB/Fasta.pm
in Bio/DB/Flat/BDB/embl.pm
in Bio/DB/Flat/BDB/fasta.pm
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
in Bio/DB/GFF/Adaptor/dbi/iterator.pm
in Bio/DB/GFF/Adaptor/memory.pm
in Bio/DB/GFF/Adaptor/memory_iterator.pm
in Bio/DB/GFF.pm
in Bio/DB/GFF/Util/Binning.pm
in Bio/DB/GFF/Util/Rearrange.pm
in Bio/Graphics/Glyph/Factory.pm
in Bio/Graphics/Util.pm
in Bio/DB/Fasta.pm
Examples
- examples/aligntutorial.pl
- examples/biblio.pl
- examples/biblio_soap.pl
- examples/blast/blast_config.pl
- examples/blast/blast_seq.pl
- examples/blast/example.table1
- examples/blast/example.table2
- examples/blast/html.pl
- examples/blast/out/BioWorkbench/blastn.txt.gz
- examples/blast/out/BioWorkbench/blastp.txt.gz
- examples/blast/out/BioWorkbench/blastx.txt.gz
- examples/blast/out/BioWorkbench/tblastn.txt.gz
- examples/blast/out/BioWorkbench/tblastx.txt.gz
- examples/blast/out/EMBL/blastn.txt.gz
- examples/blast/out/EMBL/blastp.txt.gz
- examples/blast/out/EMBL/blastx.txt.gz
- examples/blast/out/EMBL/tblastx.txt.gz
- examples/blast/out/NCBI/blastn.txt.gz
- examples/blast/out/NCBI/blastp.txt.gz
- examples/blast/out/NCBI/blastx.txt.gz
- examples/blast/out/NCBI/tblastn.txt.gz
- examples/blast/out/NCBI/tblastx.txt.gz
- examples/blast/out/WUBlast/blastn.txt.gz
- examples/blast/out/WUBlast/blastp.txt.gz
- examples/blast/out/WUBlast/blastx.txt.gz
- examples/blast/out/WUBlast/tblastn.txt.gz
- examples/blast/out/WUBlast/tblastx.txt.gz
- examples/blast/out/blastn.2.gz
- examples/blast/out/blastn.2.wu.gz
- examples/blast/out/blastp.1.gcg.gz
- examples/blast/out/blastp.1.gz
- examples/blast/out/blastp.2.gz
- examples/blast/out/blastp.2.nogap.gz
- examples/blast/out/blastp.2.wu
- examples/blast/out/blastp.205.gz
- examples/blast/out/blastp.2a.gz
- examples/blast/out/blastp.2b.gz
- examples/blast/out/blastp.email.html.gz
- examples/blast/out/blastx.2
- examples/blast/out/blastx.2.email.gz
- examples/blast/out/blastx.208.gz
- examples/blast/out/tblastn.206.out.gz
- examples/blast/parse_blast.pl
- examples/blast/parse_blast2.pl
- examples/blast/parse_multi.pl
- examples/blast/parse_positions.pl
- examples/blast/print_blasts.pl
- examples/blast/retrieve_blast.pl
- examples/blast/run_blast_remote.pl
- examples/blast/seq/acc1.dna.fasta
- examples/blast/seq/seqs.fasta
- examples/blast/seq/yal011w.dna.fasta
- examples/blast/seq/yel009c.fasta
- examples/blast/seq/ymr284w.fasta
- examples/blosum62.bla
- examples/change_gene.pl
- examples/clustalw.pl
- examples/exceptions/Error-0.13.tar.gz
- examples/exceptions/README
- examples/exceptions/test1.pl
- examples/exceptions/test2.pl
- examples/exceptions/test3.pl
- examples/exceptions/test4.pl
- examples/getGenBank.pl
- examples/gon250.bla
- examples/gsequence
- examples/hitdisplay.pl
- examples/psw.pl
- examples/remote_blast.pl
- examples/restriction.pl
- examples/rev_and_trans.pl
- examples/root_object/Bar.pm
- examples/root_object/Foo.pm
- examples/root_object/Outer.pm
- examples/root_object/destroy.pl
- examples/root_object/error.out
- examples/root_object/error.pl
- examples/root_object/filehandle.out
- examples/root_object/filehandle.pl
- examples/root_object/io.out
- examples/root_object/io.pl
- examples/root_object/read.pl
- examples/root_object/read.test
- examples/root_object/read.test2
- examples/root_object/read.test3
- examples/root_object/utilities.pl
- examples/root_object/vector/Person.pm
- examples/root_object/vector/PersonManager.pm
- examples/root_object/vector/vector.out
- examples/root_object/vector/vector.pl
- examples/run_genscan.pl
- examples/searchio/psiblast_features.pl
- examples/searchio/writer/custom_writer.pl
- examples/searchio/writer/hitwriter.pl
- examples/searchio/writer/hitwriter2.pl
- examples/searchio/writer/hitwriter3.pl
- examples/searchio/writer/hspwriter.pl
- examples/searchio/writer/rawwriter.pl
- examples/searchio/writer/resultwriter.pl
- examples/seq/id.list
- examples/seq/seq.fasta.gz
- examples/seq/seq1.fasta
- examples/seq/seq2.fasta
- examples/seq/seqs1.pl
- examples/seq/seqs2.pl
- examples/seq/seqs3.pl
- examples/seq/seqtools.pl
- examples/seq_pattern.pl
- examples/simplealign.pl
- examples/standaloneblast.pl
- examples/state-machine.pl
- examples/structure/struct_example1.pl
- examples/structure/struct_example2.pl
- examples/test-genscan.pl
- examples/use_registry.pl