Cannarozzi-Bossard, Gina M.
- Journal Article
Rights / licenseCreative Commons Attribution 2.0 Generic
Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios Show more
Journal / seriesBMC Bioinformatics
Pages / Article No.
SubjectPRIMÄRSTRUKTUR DER DESOXYRIBONUKLEINSÄUREN; DNA PRIMER + DNA TEMPLATE (MOLEKULARE GENETIK); PRIMARY STRUCTURE OF DEOXYRIBONUCLEIC ACIDS; DNA PRIMER + DNA TEMPLATE (MOLECULAR GENETICS); Codon; Synonymous Substitution; Nonsynonymous Substitution; Synonymous Mutation; Substitution Matrice
Organisational unit03309 - Gonnet, Gaston
02644 - Institut für Wissenschaftliches Rechnen, direkt
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