Nucleotide sequence codon related tools

comp_freq folder contains a Perl script for computing codon count, amino acid count, codon pair count, amino acid pair count, codon frequency (ICU), and codon context (CC) from a fasta file.

comp_score folder contains a Perl script for computing ICU score, CC score, and CAI score of sequences with respect to a reference host. It also computes the GC content, hidden stop count, exclusion sequence count, and consecutive repeats count. The sequences should be supplied in a fasta file.

For the definition of individual codon usage (ICU) and codon context (CC), please see: Chung BK, Lee DY, Computational codon optimization of synthetic gene for protein expression. BMC Syst Biol, 2012, 6:134.