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Bioinformatics Advance Access published online on August 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl430
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 6, 2006
Revised July 17, 2006
Accepted August 2, 2006

Applications note

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting

Michaël Bekaert 1, John F. Atkins 2, and Pavel V. Baranov 2 *

1 Biosciences Institute, University College Cork, Cork, Ireland
2 Biosciences Institute, University College Cork, Cork, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330, USA

* To whom correspondence should be addressed.
Pavel V. Baranov, E-mail: baranov{at}genetics.utah.edu


  Abstract

Summary: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.

Availability: The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa.

Associate Editor: Chris Stoeckert
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