BioJava

It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures.

BioJava is a tool for exploring Java's possibilities in the bioinformatics world.

What is new in this release:

• Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations.
• Improved handling of exceptions.
• Removed deprecated methods.
• Expanded the BioJava tutorial.
• Updated dependencies where applicable.
• Available on Maven Central.

What is new in version 4.0.0:

• Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations.
• Improved handling of exceptions.
• Removed deprecated methods.
• Expanded the BioJava tutorial.
• Updated dependencies where applicable.
• Available on Maven Central.

What is new in version 3.1.0:

• New Features:
• CE-CP version 1.4, with additional parameters
• Update to SCOPe 2.04
• Improvements in FASTQ parsing
• Fix bugs in PDB parsing
• Minor fixes in structure alignments

What is new in version 3.0.8:

• New:
• Genbank writer
• Parser for Karyotype file from UCSC
• Parser for Gene locations from UCSC
• Parser for Gene names file from genenames.org
• Module for Cox regression code for survival analysis
• Calculation of accessible surface area (ASA)
• Module for parsing .OBO files (ontologies)
• Improved:
• Representation of SCOP and Berkeley-SCOP classifications

What is new in version 3.0.7:

• Added a basic genbank parser.
• Fixed a problem when translating codons with N.
• Now can infer bonds in protein structures.
• Added support to parse mmcif records for organism and expression system.
• Many small bug fixes and improvements.

What is new in version 3.0.6:

• Development moved to GitHub at: https://github.com/biojava/biojava

What is new in version 3.0.5:

• New parser for CATH classification.
• New parser for Stockholm file format.
• Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit.
• Several bug fixes.

What is new in version 3.0.4:

• This is mainly a bug fix release addressing issues in the protein structure and disorder modules.
• One new feature: SCOP data can now be either accessed from the original SCOP site in the UK or the Berkeley version.

What is new in version 3.0.3:

• Significant improvements to the web service module (ncbi blast and hmmer web services).
• "New" fastq parser (ported from the biojava 1 series to version 3).
• Support for SIFTS-PDB to UniProt mapping.
• Protmod module renamed to modfinder.

What is new in version 3.0.2:

• protein-structure: Improved handling of protein domains: Now supports SCOP. New functionality for automated prediction of protein domains, based on Protein Domain Parser.
• Minor improvements and bug fixes in several other modules.
• biojava3-aa-prop: This new module allows the calculation of physico chemical and other properties of protein sequences.
• biojava3-protein-disorder: A new module for the prediction of disordered regions in proteins. It based on a Java implementation of the RONN predictor.

What is new in version 3.0.1:

• The 3.0.1 release is mainly a bug fix release for the recent 3.0 released which provided a major rewrite of the biojava code base.

Requirements:

• Java 1.6 or higher