ArticleAlgorithms for molecular biology : AMB2010
Back-translation for discovering distant protein homologies in the presence of frameshift mutations.
Article in Algorithms for molecular biology : AMB, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 15 citations in OpenAlex.
- Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Aligning coding sequences with frameshift extension penalties.Algorithms for molecular biology : AMB · 2017Article
- Frameshift alignment: statistics and post-genomic applications.Bioinformatics (Oxford, England) · 2014Article
- Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins.PLoS genetics · 2013Article
- HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFrameshift 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.
resultsWe 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/].
conclusionsOur approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.