[Biojava-l] BioJava 3.0 released

[Andreas Prlic]

BioJava 3.0 has been released and is available from
http://biojava.org/wiki/BioJava:Download .

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

Over the last year BioJava has undergone a major re-write. It has been
modularized into small, re-usable components and a number of new
features have been added. The new approach, modeled after the apache
commons, minimizes dependencies and allows for easier contribution of
new components.

At the present the main modules are:

biojava3-core: The core module offers the basic tools required for
working with biological sequences of various types (DNA, RNA,
protein). Besides file parsers for popular file formats it provides
efficient data structures for sequence manipulation and serialization.

biojava3-genome: The genome module provides support for reading and
writing of gtf, gff2, gff3 file formats

biojava3-alignment: This module provides implementations for pairwise
and multiple sequence alignments (MSA). The implementation for MSA
provides a flexible and multi-threaded framework that works in linear
space and that, as an option, allows the users to define anchors that
are used in the build up of the multiple alignment.

biojava3-structure: The 3D protein structure module provides parsers
and a data model for working PDB and mmCif files. New features in this
release are the implementation of the CE and FATCAT structural
alignment algorithms and the support of chemical component definition
files, for a chemically and biologically correct representation of
modified residues and ligands.

biojava3-protmod: The protein modification module can detect more than
200 protein modifications and crosslinks in 3D protein structures. It
comes with an XML file and Java data structures to store information
about different types of protein modifications collected from PDB,
RESID, and PSI-MOD.

Not every feature of the BioJava 1.X code base was migrated over to
BioJava 3.0. A modularized version of the 1.X sources is available as
a new "biojava-legacy" project.

Thanks to all contributors for making this release possible.

Happy Biojava-ing,

Andreas