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Nucleic Acids Research Advance Access published online on December 14, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl1026
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy

Keith Knapp1,* and Yi-Ping Phoebe Chen1,2,*

1 Faculty of Science and Technology, Deakin University Australia 2 Australia Research Council Centre in Bioinformatics Australia

*To whom correspondence should be addressed. Tel: +61 3 92517684; Fax: +61 3 92517604; Email: phoebe.chen{at}deakin.edu.au

Received September 21, 2006. Revised November 13, 2006. Accepted November 13, 2006.

We present an independent evaluation of six recent hidden Markov model (HMM) genefinders. Each was tested on the new dataset (FSH298), the results of which showed no dramatic improvement over the genefinders tested five years ago. In addition, we introduce a comprehensive taxonomy of predicted exons and classify each resulting exon accordingly. These results are useful in measuring (with finer granularity) the effects of changes in a genefinder. We present an analysis of these results and identify four patterns of inaccuracy common in all HMM-based results.

*Correspondence may also be addressed to Keith Knapp. Tel: +61 3 52272606; Fax: +61 3 52272167; Email: kdk{at}deakin.edu.au


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