Back-translation for discovering distant protein homologies - Inria - Institut national de recherche en sciences et technologies du numérique Accéder directement au contenu
Communication Dans Un Congrès Année : 2009

Back-translation for discovering distant protein homologies

Résumé

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.
Fichier principal
Vignette du fichier
patharticle.pdf (186.67 Ko) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

inria-00448741 , version 1 (25-01-2010)

Identifiants

Citer

Marta L. Gîrdea, Laurent Noé, Gregory Kucherov. Back-translation for discovering distant protein homologies. the 9th International Workshop in Algorithms in Bioinformatics (WABI), Sep 2009, Philadelphia, United States. pp.108-120, ⟨10.1007/978-3-642-04241-6_10⟩. ⟨inria-00448741⟩
164 Consultations
135 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More