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Bioinformatics Advance Access originally published online on November 22, 2007
Bioinformatics 2008 24(2):172-175; doi:10.1093/bioinformatics/btm573
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences

Dean Laslett 1 and Björn Canbäck 2,*

1Murdoch University, Perth, Western Australia, Australia and 2Björn Canbäck Bioinformatik, Vindögatan 66, 257 33 Rydebäck, Sweden

*To whom correspondence should be addressed.


  Abstract

Motivation: Mitochondrial genomes encode their own transfer RNAs (tRNAs). These are often degenerate in sequence and structure compared to tRNAs in their bacterial ancestors. This is one of the reasons why current tRNA gene predictor programs perform poorly identifying mitochondrial tRNA genes. As a consequence there is a need for a new program with the specific aim of predicting these tRNAs.

Results: In this study, we present the software ARWEN that identifies tRNA genes in metazoan mitochondrial nucleotide sequences. ARWEN detects close to 100% of previously annotated genes.

Availability: An online version, software for download and test results are available at www.acgt.se/online.html

Contact: bcanback{at}acgt.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on June 21, 2007; revised on November 13, 2007; accepted on November 13, 2007

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