Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2010-01-26
Algorithms in Bioinformatics, 2009, LNBI 5724 : 108-120
Biology
Quantitative Biology
Quantitative Methods
The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009)
Scientific paper
10.1007/978-3-642-04241-6_10
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.
Gîrdea Marta L.
Kucherov Gregory
Noé Laurent
No associations
LandOfFree
Back-translation for discovering distant protein homologies does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Back-translation for discovering distant protein homologies, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Back-translation for discovering distant protein homologies will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-644144