1. BioJava: an open-source framework for bioinformatics in 2012
- Author
-
Prlić, Andreas, Yates, Andrew, Bliven, Spencer E, Rose, Peter W, Jacobsen, Julius, Troshin, Peter V, Chapman, Mark, Gao, Jianjiong, Koh, Chuan Hock, Foisy, Sylvain, Holland, Richard, Rimša, Gediminas, Heuer, Michael L, Brandstätter–Müller, H, Bourne, Philip E, and Willis, Scooter
- Subjects
Networking and Information Technology R&D (NITRD) ,Amino Acids ,Computational Biology ,Genomics ,Protein Conformation ,Protein Processing ,Post-Translational ,Proteins ,Sequence Alignment ,Sequence Analysis ,Sequence Analysis ,DNA ,Sequence Analysis ,Protein ,Software ,Mathematical Sciences ,Biological Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
UnlabelledBioJava 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.ResultsBioJava 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.AvailabilityBioJava 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.
- Published
- 2012