Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Sep 15;24(18):2096-7.
doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.

BioJava: an open-source framework for bioinformatics

R C G Holland  1 , T A Down, M Pocock, A Prlić, D Huen, K James, S Foisy, A Dräger, A Yates, M Heuer, M J Schreiber
Affiliations

BioJava: an open-source framework for bioinformatics

R C G Holland et al. Bioinformatics. .

Abstract

Summary: 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.

Availability: 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 1.5 or higher. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Loading a GenBank file with BioJava and writing it out as FASTA. The example demonstrates the use of several convenience methods that hide the bulk of the implementation. If the developer desires a more flexible parser it is possible to make use of the interfaces hidden behind the convenience methods to expose a fully customizable, multi-component, event-based parsing model.
See this image and copyright information in PMC

References

    1. Altschul SF, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Berman HM, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. - PMC - PubMed
    1. Pocock M. PhD thesis. Cambridge, UK: University of Cambridge; 2003. Computational analysis of genomes.
    1. Pocock M, et al. BioJava: open source components for bioinformatics. ACM SIGBIO Newsl. 2000;20:10–12.
    1. Ewing B, et al. Base-calling of automated sequencer traces using phred. Genome Res. 1998;8:175–185. - PubMed

Publication types