title: An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy.
abstract: 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.
authors.affiliation: Faculty of Science and Technology, Deakin University, Australia. kdk@deakin.edu.au
authors.forename: Keith
authors.initials: K
authors.lastname: Knapp
authors.forename: Yi-Ping Phoebe
authors.initials: YP
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods; D003627:Data Interpretation, Statistical; D005091:Exons; D005796:Genes; D006801:Humans; D008390:Markov Chains; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software