I have a set of homologous gene pairs from two complete bacterial genomes. I also have the whole chromosome and GFF files of gene locations. I want to find the coordinates for non-synonymous SNPs in each gene relative to its homolog.
Is there a tool where I can feed the gene pairs or even better chromosome+GFF and get non-synonymous SNP positions back?
This is simple enough to script using blast or clustal but checking just in case there is something out there. I was not able to find a BioPerl module or tool for this but maybe I missed something obvious. Thanks much!