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Bioinformatics Advance Access published online on April 4, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl076
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 3, 2005
Revised February 18, 2006
Accepted February 27, 2006

Article

Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans

Ritesh Agrawal 1 and Gary D. Stormo 1 *

1 Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA

* To whom correspondence should be addressed.
Gary D. Stormo, E-mail: stormo{at}genetics.wustl.edu


  Abstract

Motivation: Computational gene prediction methods are an important component of whole genome analyses. While ab initio gene finders have demonstrated major improvements in accuracy, the most reliable methods are evidence-based gene predictors. These algorithms can rely on several different sources of evidence including predictions from multiple ab initio gene finders, matches to known proteins, sequence conservation, and partial cDNAs to predict the final product. Despite the success of these algorithms, prediction of complete gene structures, especially for alternatively spliced products, remains a difficult task.

Results: LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a new evidence-based gene finding algorithm which integrates a length-constraint into a dynamic programming-based framework for prediction of gene products. On a C. elegans test set of alternatively spliced internal exons, its performance exceeds that of current ab initio gene finders and in most cases can accurately predict the correct form of all the alternative products. As the length information used by the algorithm can be obtained in a high-throughput fashion, we propose that integration of such information into a gene-prediction pipeline is feasible and doing so may improve our ability to fully characterize the complete set of mRNAs for a genome.

Availability: LOCUS is available from http://ural.wustl.edu/software.html.

Associate Editor: Martin Bishop
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