Bioperl 1.0 Release Announcement

I am pleased to announce the release of verision 1.0 of the Bioperl toolkit. This release represents what we believe to be feature complete for most biological sequence manipulations in bioinformatics. A great deal of work has gone into this project from its start in 1995 as a collection of modules for sequences and alignments to its transition to a more formal Object Oriented framework which has allowed for easier extensibility for the myriad of data formats in the realm of bioinformatics. Work in the past year has seen an explosion of new areas of interest by developers as well as a commitment to stability and an easy to use programming interface.

This release of the toolkit contains modules for representing biological sequences, protein structure, sequence alignments, BLAST and FastA reports, biological maps, sequence features and their locations including complex locations, annotations & bibliographic references, phylogenetic trees, and gene structures. Included in the kit are tools to visually render sequences, build and access local sequence indexes, parse and output most major biological sequence formats, access to bibliographic query services,
query access to remote sequence databases over the web, input and output of biological maps, and support for phylogenetic trees. Additionally the toolkit supports representations of sequence variations and mutations to allow a programming interface to sequences with variable residues.

This release would not have been possible without the hard work of all the members of the project. These include the Bioperl Core: Ewan Birney, Chris Dagdigian, Hilmar Lapp, Heikki Lehvaslaiho, Jason Stajich, and Lincoln Stein. Significant contributions of code, debugging, and suggestions were made by all the members of the project and list subscribers especially: Dave Block, Kris Boulez, Steve Chervitz, Michele Clamp, James Cuff, Allen Day, James Diggans, Aaron Mackey, Chris Mungall, Brian Osborne, Peter Schattner, Martin Senger, Elia Stupka, and Mark Wilkinson. Additionally the project has recieved help from many of the mailing list subscribers and bioperl users with their suggestions and questions which has helped shaped the
development effort. The project has also greatly benefited from the cross-talk between the Biopython and BioJava projects and we'd like to acknowledge their support and idea sharing.

We'd also like to thank especially thank Brian Osborne and Peter Schattner for their work in getting the documentation and Bioperl Tutorial updated for all the new modules and features.

Jason Stajich on behalf of the Bioperl Core.

The release is available at or from the website and will be available from CPAN in the coming week.

Please see the INSTALL and README documents for information about installing and cross-platform compatibilities.

The code is released under the Perl Artistic License which is included in the distribution file.

Bioperl is supported by the Open Bioinformatics Foundation
( which provides infrastructure for the projects.

You can provide feedback to the project and help us estimate the number of users the project has by responding to the bioperl survey. Go to to help us gauge how useful the toolkit is to your work and where we can make improvements to address new areas of computational biology and bioinformatics.


1.0.0 Major Stable Release

This represents a major release of bioperl with significant improvements over the 0.7.x series of releases.

Bio::Biblio contains modules for Bibliographic data.
Bio::DB::Biblio contains the query modules. Additionally one can parse medlinexml from the ebi bibliographic query service (BQS)
system and Pubmed xml from NCBI. See Martin Senger's documentation in Bio::Biblio for more information.

Bio::DB::Registry is a sequence database registry part of Open Bioinformatics Database Access. Additionally Bio::DB::Flat was
introduced to support the cross-project OBDA standard for indexed flatfiles. See for more
information. This project is under active development so the modules in this release represent preliminary implementations.

File-based and In-Memory Sequence caching is provided by Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
local database.

Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has been added by Lincoln Stein.

XEMBL SOAP service access in provided in Bio::DB::XEMBL.

Bio::Map and Bio::MapIO for biological map navigation and a framework afor parsing them in.

Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
Future work will integrate Pasteur Institute's Pise and EBI's openBSA analysis queues for remote analysis.

Bio::AnnotationCollectionI and Bio::Annotation::Collection introduced as new objects for handling Sequence Annotation
information (dblinks, references, etc) and is more robust that previous annotation handling object.

Bio::SearchIO was introduced to support an extensible framework for sequence database search results. Currently blast, NCBI XML blast format (-m 7), and FastA parsing are implemented. The Bio::Search objects were added to represent the Result, Hit, and
HSP objects retrieved from a search. To support this new direction Bio::Tools::Blast is officially deprecated.

Bio::SearchIO::Writer system allows output of Bio::Search objects in a tabular or HTML form.

Bio::DB::GFF is Lincoln Stein's database implementation of GFF files which can be used for DAS backends and is part of the Generic Model Organism Database project (

Bio::Tree and Bio::TreeIO namespaces and modules were added to support representation and parsing of phylogenetic trees.

Bio::Structure as added in 0.9.1 and includes a pdb parser and objects to represent protein structure.

More Multiple Sequence formats have been added for parsing or writing.

The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
Bio::LocationI objects as well as start/end.

Bio::SimpleAlign now supports two methods for calculating average and overall percentage identity.

30% speedup was achieved in SeqIO genbank and embl parsers, future releases will focus on an event based parsing system
where we hope to achieve improved parsing speeds.

A FAQ has been started and is included in the release to provide a starting point for frequent questions and issues.

Jason Stajich
Duke University
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