Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Back-translation for discovering distant protein homologies in the presence of frameshift mutations. | Gírdea et al. Algorithms for Molecular Biology 2010 5 6 http content 5 1 6 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Back-translation for discovering distant protein homologies in the presence of frameshift mutations Marta Girdea1 2 Laurent Noé1 2 Gregory Kucherov1 2 3 Abstract Background 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. Results We developed 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. Our implementation is freely available at http path . Conclusions Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods which is confirmed by biologically significant examples. Background Context and motivation In protein-coding DNA sequences frameshift mutations insertions or deletions of one or more bases can alter the translation reading frame affecting all the amino acids encoded from that point forward. Thus frameshifts produce a drastic change in the resulting protein sequence preventing any similarity to be visible at the amino acid level. For that reason classic protein alignment methods that rely on amino acid comparisons fail to reveal the proteins common origins in the case of divergence by .
