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Bioinformatics Advance Access originally published online on March 11, 2009
Bioinformatics 2009 25(10):1331-1332; doi:10.1093/bioinformatics/btp141
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes

Micah Hamady 1, Stephanie A. Wilson 2, Jesse Zaneveld 3, Noboru Sueoka 4 and Rob Knight 5,*

1Department of Computer Science, University of Colorado, Boulder, CO 80309, 2AmGen, 4000 Nelson Rd, Longmont, CO 80503, 3Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, 4Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 and 5Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA

*To whom correspondence should be addressed.


  Abstract

DNA composition in general, and codon usage in particular, is crucial for understanding gene function and evolution. CodonExplorer, available online at http://bmf.colorado.edu/codonexplorer/, is an online tool and interactive database that contains millions of genes, allowing rapid exploration of the factors governing gene and genome compositional evolution and exploiting GC content and codon usage frequency to identify genes with composition suggesting high levels of expression or horizontal transfer.

Contact: rob{at}spot.colorado.edu

Associate Editor: Limsoon Wong

Received on February 20, 2009; revised on March 6, 2009; accepted on March 8, 2009

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