The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
bioperl-0.6.1
++

Changes for version 0.6.1

  • o Sequences can have Sequence Features attached to them
    • The sequence features can be read from or written to EMBL and GenBank style flat files
  • o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided
  • o A Species object to represent nodes on a taxonomy tree is provided
  • o The ability to parse HMMER and Sim4 output has been added
  • o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour.
  • o Flat file indexed databases provide both random access and sequential access to their component sequences.
  • o A CodonTable object has been written with all known CodonTables accessible.
  • o A number of new lightweight analysis tools have been added, such as molecular weight determination.
    • The 0.6 release also has improved software engineering
  • o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects
  • o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I').
    • This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl.
  • o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments.
  • o Many more tests have been added (a total of 172 automatic tests are now run before release).

Documentation

bioperl
Bioperl
Design Documentation
Bioperl
Coordinated OOP-Perl Modules for Biology
Bioperl
Getting Started
bpfetch.pl
fetches sequences from bioperl indexed databases
bpindex.pl
indexes files for use by bpfetch

Modules

Bio::Annotation
A generic object for annotations
Bio::Annotation::Comment
A Comment on an Annotation
Bio::Annotation::DBLink
Database Link
Bio::Annotation::Reference
Literature Reference Block
Bio::DB::Ace
Database object interface to ACeDB servers
Bio::DB::GenBank
Database object interface to GenBank
Bio::DB::GenPept
Database object interface to GenPept
Bio::DB::RandomAccessI
Abstract interface for a sequence database
Bio::DB::SeqI
Abstract Interface for Sequence databases
Bio::Index::Abstract
Abstract interface for indexing a flat file
Bio::Index::AbstractSeq
Base class for AbstractSeq's
Bio::Index::EMBL
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Bio::Index::Fasta
Interface for indexing (multiple) fasta files
Bio::Index::SwissPfam
Interface for indexing swisspfam files
Bio::LocatableSeq
A Sequence object with start/end points on it
Bio::PrimarySeq
Bioperl lightweight Sequence Object
Bio::PrimarySeqI
Interface definition for a Bio::PrimarySeq
Bio::Range
Pure perl RangeI implementation
Bio::RangeI
Range interface
Bio::Root::Err
Exception class for Perl 5 objects
Bio::Root::Global
Global variables and utility functions
Bio::Root::IOManager
Input and output manager for Perl5 objects.
Bio::Root::Object
A core Perl 5 object.
Bio::Root::RootI
Abstract interface to root object code
Bio::Root::Utilities
General-purpose utility module
Bio::Root::Vector
Interface for managing linked lists of Perl5 objects.
Bio::Root::Xref
A generic cross-reference object.
Bio::Search::Hit::Fasta
Hit object specific for Fasta-generated hits
Bio::Search::Hit::HitI
Abstract interface for Hit objects
Bio::Search::Processor
DESCRIPTION of Object
Bio::Search::Processor::Fasta
Processor of Fasta-generated data streams
Bio::Search::Processor::ProcessorI
Abstract Interface for Processor Objects
Bio::Search::Result::Fasta
Result object for FASTA-generated data sources
Bio::Search::Result::ResultI
Abstract interface to Result objects
Bio::SearchDist
A perl wrapper around Sean Eddy's histogram object
Bio::Seq
Sequence object, with features
Bio::SeqFeature::FeaturePair
hold pair feature information e.g. blast hits
Bio::SeqFeature::Generic
Generic SeqFeature
Bio::SeqFeatureI
Abstract interface of a Sequence Feature
Bio::SeqI
Abstract Interface of Sequence (with features)
Bio::SeqIO
Handler for SeqIO Formats
Bio::SeqIO::FTHelper
Helper class for Embl/Genbank feature tables
Bio::SeqIO::MultiFile
Treating a set of files as a single input stream
Bio::SeqIO::embl
EMBL sequence input/output stream
Bio::SeqIO::fasta
fasta sequence input/output stream
Bio::SeqIO::gcg
GCG sequence input/output stream
Bio::SeqIO::genbank
GenBank sequence input/output stream
Bio::SeqIO::pir
PIR sequence input/output stream
Bio::SeqIO::raw
raw sequence file input/output stream
Bio::SeqIO::scf
SCF sequence input/output stream
Bio::SeqIO::swiss
Swissprot sequence input/output stream
Bio::SimpleAlign
Multiple alignments held as a set of sequences
Bio::Species
Generic species object
Bio::Tools::AlignFactory
Base object for alignment factories
Bio::Tools::Blast
Bioperl BLAST sequence analysis object
Bio::Tools::Blast::HSP
Bioperl BLAST High-Scoring Segment Pair object
Bio::Tools::Blast::HTML
Bioperl Utility module for HTML formatting Blast reports
Bio::Tools::Blast::Run::LocalBlast
Bioperl module for running Blast analyses locally.
Bio::Tools::Blast::Run::Webblast
Bioperl module for running Blast analyses using a HTTP interface.
Bio::Tools::Blast::Sbjct
Bioperl BLAST "Hit" object
Bio::Tools::CodonTable
Bioperl codon table object
Bio::Tools::Fasta
Bioperl Fasta utility object
Bio::Tools::HMMER::Domain
One particular domain hit from HMMER
Bio::Tools::HMMER::Results
Object representing HMMER output results
Bio::Tools::HMMER::Set
Set of identical domains from HMMER matches
Bio::Tools::IUPAC
Generates unique Seq objects from an ambiguous Seq object
Bio::Tools::RestrictionEnzyme
Bioperl object for a restriction endonuclease object.
Bio::Tools::SeqAnal
Bioperl sequence analysis base class.
Bio::Tools::SeqPattern
Bioperl object for a sequence pattern or motif
Bio::Tools::SeqStats
Object holding statistics for one particular sequence
Bio::Tools::SeqWords
Object holding n-mer statistics for one sequence
Bio::Tools::Sigcleave
Bioperl object for sigcleave analysis
Bio::Tools::Sim4::Exon
A single
Bio::Tools::Sim4::Results
Results of one Sim4 run
Bio::Tools::WWW
Bioperl manager for web resources related to biology.
Bio::Tools::pSW
DESCRIPTION of Object
Bio::UnivAln
Bioperl alignment object

Examples

Other files