Computational protocol: Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content

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[…] Orthologous gene pairs between each genome pair were identified based on reciprocal best hits using the protein-protein BLAST service Blastp (https://blast.ncbi.nlm.nih.gov/Blast.cgi), with criteria of E <10−5, 80% minimum residues that could be aligned, and 30% identity. Protein sequences encoded by identified orthologous gene pairs were aligned with ClustalW, and then back-translated into nucleotide sequences based on their original sequences. Numbers of substitutions per nonsynonymous site (Ka) and numbers of substitutions per synonymous site (Ks) were calculated following Yang’s definition using the PAML package, with default parameters. […]

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