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Nucleic Acids Research
Vol. 35, No. 1, 2007; Pages: 317–324

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

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

Faculty of Science and Technology, Deakin University, Australia.


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.

Keywords:exon taxonomy;hidden Markov model;Poly(A) tails;exons;introns;whole-genome;ab initio;homology;taxonomy.

Corresponding author: Tel +61 3 92517684; Fax +61 3 92517604

E-mail: phoebe.chen@deakin.edu.au


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