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

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...

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Detalles Bibliográficos
Autores principales: Knapp, Keith, Chen, Yi-Ping Phoebe
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Survey and Summary
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802560/
https://www.ncbi.nlm.nih.gov/pubmed/17170005
http://dx.doi.org/10.1093/nar/gkl1026
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author Knapp, Keith
Chen, Yi-Ping Phoebe
author_facet Knapp, Keith
Chen, Yi-Ping Phoebe
author_sort Knapp, Keith
collection PubMed
description 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.
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spelling pubmed-18025602007-03-01 An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy Knapp, Keith Chen, Yi-Ping Phoebe Nucleic Acids Res Survey and Summary 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. Oxford University Press 2007-01 2006-12-14 /pmc/articles/PMC1802560/ /pubmed/17170005 http://dx.doi.org/10.1093/nar/gkl1026 Text en © 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.
spellingShingle Survey and Summary
Knapp, Keith
Chen, Yi-Ping Phoebe
An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title_full An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title_fullStr An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title_full_unstemmed An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title_short An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
title_sort evaluation of contemporary hidden markov model genefinders with a predicted exon taxonomy
topic Survey and Summary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802560/
https://www.ncbi.nlm.nih.gov/pubmed/17170005
http://dx.doi.org/10.1093/nar/gkl1026
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