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• W2078939975 abstract "A widely used algorithm for computing an optimal local alignment between two sequences requires a parameter set with a substitution matrix and gap penalties. It is recognized that a proper parameter set should be selected to suit the level of conservation between sequences. We describe an algorithm for selecting an appropriate substitution matrix at given gap penalties for computing an optimal local alignment between two sequences. In the algorithm, a substitution matrix that leads to the maximum alignment similarity score is selected among substitution matrices at various evolutionary distances. The evolutionary distance of the selected substitution matrix is defined as the distance of the computed alignment. To show the effects of gap penalties on alignments and their distances and help select appropriate gap penalties, alignments and their distances are computed at various gap penalties. The algorithm has been implemented as a computer program named SimDist. The SimDist program was compared with an existing local alignment program named SIM for finding reciprocally best-matching pairs (RBPs) of sequences in each of 100 protein families, where RBPs are commonly used as an operational definition of orthologous sequences. SimDist produced more accurate results than SIM on 50 of the 100 families, whereas both programs produced the same results on the other 50 families. SimDist was also used to compare three types of substitution matrices in scoring 444,461 pairs of homologous sequences from the 100 families." @default.
• W2078939975 created "2016-06-24" @default.
• W2078939975 creator A5022987905 @default.
• W2078939975 date "2008-03-01" @default.
• W2078939975 modified "2023-10-16" @default.
• W2078939975 title "Sequence Alignment with an Appropriate Substitution Matrix" @default.
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• W2078939975 doi "https://doi.org/10.1089/cmb.2007.0155" @default.
• W2078939975 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18312146" @default.
• W2078939975 hasPublicationYear "2008" @default.
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