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A New Phylo-HMM Paradigm to Search for Sequences

Jean-Baka Domelevo Entfellner 1, * Olivier Gascuel 2
* Corresponding author
1 LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : We introduce a new type of phylogenetic Hidden Markov Model, combining the strength of usual HMM and the knowledge of the phylogeny of a family of sequences. We use such models to look into the genome of a target species for members of the sequence family. Our results on some 690 protein families show a better sensitivity and a better specificity when compared to standard profile HMM or Blast searchs.
Keywords : homology Genomics sequences HMM phylo-HMM phylogeny models
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Conference papers
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-00324458
Contributor : Jean-Baka Domelevo Entfellner <>
Submitted on : Thursday, September 25, 2008 - 10:00:02 AM
Last modification on : Thursday, May 24, 2018 - 3:59:22 PM

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  • HAL Id : lirmm-00324458, version 1

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CNRS | MAB | LIRMM | MIPS | UNIV-MONTPELLIER

Citation

Jean-Baka Domelevo Entfellner, Olivier Gascuel. A New Phylo-HMM Paradigm to Search for Sequences. MIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, Saint Martin de Londres, France. ⟨lirmm-00324458⟩

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