BioJava

Software screenshot:
BioJava
Software detaljer:
Version: 4.1.0 Opdateret
Upload dato: 10 Dec 15
Licens: Gratis
Popularitet: 172

Rating: 1.0/5 (Total Votes: 1)

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

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