title: BioJava: an open-source framework for bioinformatics in 2012.
abstract: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.
  
  
  RESULTS
  BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.
  
  
  BACKGROUND
  BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.
authors.affiliation: San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA. andreas.prlic@gmail.com
authors.forename: Andreas
authors.initials: A
authors.lastname: Prlić
authors.forename: Andrew
authors.initials: A
authors.lastname: Yates
authors.forename: Spencer E
authors.initials: SE
authors.lastname: Bliven
authors.forename: Peter W
authors.initials: PW
authors.lastname: Rose
authors.forename: Julius
authors.initials: J
authors.lastname: Jacobsen
authors.forename: Peter V
authors.initials: PV
authors.lastname: Troshin
authors.forename: Mark
authors.initials: M
authors.lastname: Chapman
authors.forename: Jianjiong
authors.initials: J
authors.lastname: Gao
authors.forename: Chuan Hock
authors.initials: CH
authors.lastname: Koh
authors.forename: Sylvain
authors.initials: S
authors.lastname: Foisy
authors.forename: Richard
authors.initials: R
authors.lastname: Holland
authors.forename: Gediminas
authors.initials: G
authors.lastname: Rimsa
authors.forename: Michael L
authors.initials: ML
authors.lastname: Heuer
authors.forename: H
authors.initials: H
authors.lastname: Brandstätter-Müller
authors.forename: Philip E
authors.initials: PE
authors.lastname: Bourne
authors.forename: Scooter
authors.initials: S
authors.lastname: Willis
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D023281:Genomics; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017421:Sequence Analysis; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins