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CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.
Noutahi, Emmanuel; Calderon, Virginie; Blanchette, Mathieu; Lang, Franz B; El-Mabrouk, Nadia.
Afiliación
  • Noutahi E; Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada.
  • Calderon V; Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada.
  • Blanchette M; School of Computer Science, McGill University, McConnell Engineering Bldg., Montréal, QC H3A 0E9, Canada.
  • Lang FB; Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Montréal, QC CP 6128, Canada.
  • El-Mabrouk N; Département d'Informatique et de Recherche Opérationnelle (DIRO), Université de Montréal, Montréal, QC CP 6128, Canada.
Bioinformatics ; 33(21): 3331-3339, 2017 Nov 01.
Article en En | MEDLINE | ID: mdl-28655158
MOTIVATION: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives. RESULTS: We present CoreTracker, a new algorithm for the inference of sense-to-sense codon reassignments. CoreTracker identifies potential codon reassignments in a set of related genomes, then uses statistical evaluations and a random forest classifier to predict those that are the most likely to be correct. Predicted reassignments are then validated through a phylogeny-aware step that evaluates the impact of the new genetic code on the protein alignment. Handling simultaneously a set of genomes in a phylogenetic framework, allows tracing back the evolution of each reassignment, which provides information on its underlying mechanism. Applied to metazoan and yeast genomes, CoreTracker significantly outperforms existing methods on both precision and sensitivity. AVAILABILITY AND IMPLEMENTATION: CoreTracker is written in Python and available at https://github.com/UdeM-LBIT/CoreTracker. CONTACT: mabrouk@iro.umontreal.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Codón / Núcleo Celular / Análisis de Secuencia de ADN / Genómica / Genoma Mitocondrial Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Animals Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2017 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Codón / Núcleo Celular / Análisis de Secuencia de ADN / Genómica / Genoma Mitocondrial Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Animals Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2017 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido