ArticleAlgorithms for molecular biology : AMB2017
Aligning coding sequences with frameshift extension penalties.
Article in Algorithms for molecular biology : AMB, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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- From pairwise to multiple spliced alignment.Bioinformatics advances · 2022Article
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6 authors at 1 institution in 1 country.
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Abstract
backgroundFrameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene coding regions. Frameshift translations can be identified by aligning two CDS, from a same gene or from homologous genes, while accounting for their codon structure. Two main classes of algorithms have been proposed to solve the problem of aligning CDS, either by amino acid sequence alignment back-translation, or by simultaneously accounting for the nucleotide and amino acid levels. The former does not allow to account for frameshift translations and up to now, the latter exclusively accounts for frameshift translation initiation, not considering the length of the translation disruption caused by a frameshift.
resultsWe introduce a new scoring scheme with an algorithm for the pairwise alignment of CDS accounting for frameshift translation initiation and length, while simultaneously considering nucleotide and amino acid sequences. The main specificity of the scoring scheme is the introduction of a penalty cost accounting for frameshift extension length to compute an adequate similarity score for a CDS alignment. The second specificity of the model is that the search space of the problem solved is the set of all feasible alignments between two CDS. Previous approaches have considered restricted search space or additional constraints on the decomposition of an alignment into length-3 sub-alignments. The algorithm described in this paper has the same asymptotic time complexity as the classical Needleman-Wunsch algorithm.
conclusionsWe compare the method to other CDS alignment methods based on an application to the comparison of pairs of CDS from homologous
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