Computational protocol: Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces

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[…] Sixty-eight bacterial strains were used to assess the phylogeny of DinB and DnaE homologs in them. These sequences were retrieved from KEGG Orthology (KO) database (http://www.genome.jp/kegg/ko.html). The homologous sequences were aligned using MAFFT (PMID: 18372315, PMID: 16362903, PMID: 15661851), and the aligned sequences were used to reconstruct the phylogenetic trees in a maximum-likelihood manner with PhyML (PMID: 14530136). To acquire accurate and reliable phylogeny, equilibrium frequencies and proportion of invariable sites were optimized and estimated in the substitution model. In addition, the tree topology was searched using SPR moves (PMID: 16234323). For evaluation of the branching significance, the aLRT statistical test was applied to compute the branch supports (PMID: 16785212). [...] The coding sequences of dinB and dnaE were retrieved from KEGG Orthology (KO) database (http://www.genome.jp/kegg/ko.html), and aligned by the codon-based alignment using MAFFT and RevTrans (PMID: 18372315, PMID: 16362903, PMID: 15661851, PMID: 12824361). The Li93 method (PMID: 8433381) was then exploited to calculate the Ka/Ks values. For sliding Ka/Ks calculations, the windows size was 90 bases and the step was 15 bases. […]

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