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Back-translation for discovering distant protein homologies in the presence of frameshift mutations.

Girdea M, Noe L, Kucherov G - Algorithms Mol Biol (2010)

Bottom Line: 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.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.

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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://bioinfo.lifl.fr/path/].

Conclusions: Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.

No MeSH data available.


Obtaining a simple back-translation graph for the amino acid R. The construction of a simple back-translation graph, for the amino acid R, encoded by 6 codons, is illustrated here. Note that identical nucleotides are associated to different nodes if they have different prefixes in the codons where they appear.
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Figure 2: Obtaining a simple back-translation graph for the amino acid R. The construction of a simple back-translation graph, for the amino acid R, encoded by 6 codons, is illustrated here. Note that identical nucleotides are associated to different nodes if they have different prefixes in the codons where they appear.

Mentions: The construction of a simple back-translation graph for the amino acid R is illustrated in Figure 2.


Back-translation for discovering distant protein homologies in the presence of frameshift mutations.

Girdea M, Noe L, Kucherov G - Algorithms Mol Biol (2010)

Obtaining a simple back-translation graph for the amino acid R. The construction of a simple back-translation graph, for the amino acid R, encoded by 6 codons, is illustrated here. Note that identical nucleotides are associated to different nodes if they have different prefixes in the codons where they appear.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2821327&req=5

Figure 2: Obtaining a simple back-translation graph for the amino acid R. The construction of a simple back-translation graph, for the amino acid R, encoded by 6 codons, is illustrated here. Note that identical nucleotides are associated to different nodes if they have different prefixes in the codons where they appear.
Mentions: The construction of a simple back-translation graph for the amino acid R is illustrated in Figure 2.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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://bioinfo.lifl.fr/path/].

Conclusions: Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.

No MeSH data available.