PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies).
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Lin MF, Jungreis I, and Kellis M (2011).
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions.
Bioinformatics (2011) 27 (13): i275-i282.