Codon_counter-V1.pl

The script will count the number of codons in every gene in each fasta file of the folder and produce a result file for each genome containing the fraction of codons of each gene that correspond to each codon. Genes annotated as pseudogenes or presenting a number of nucleotides not dividable by three are not considered. The program is designed to use the “_cds_from_genomic.fna” files from GeneBank or RefSeq that have fasta headers in genebank format. This allows the script to recognize genes annotated with the “pseudo” flag as “true”. In order to work, the script requires the text that will be added to each result file and a file with the list of codons that it should look for. We have added a sample file named codons.txt that contains all possible codons, but users may want to erase stop codons from the list.

Usage: perl Codon_counter-V1.pl