New to the forums and new to bioinformatics. Working on comparative genomics and need to analyze SNPs in two closely related species. I have a list of SNPs parsed from the 454 difference data of a fully sequenced and annotated bacterial genome. Need to compare it to 454 contigs of a cryptic species.
Want to find
1. direction of SNPs in cryptic species (CG to AT or AT to GC)
2. coding position of SNPs
What is the best way to go about this?
There are a total of ~120 SNPs that blast to the cryptic species contigs, but some hit more than once. I have been using stand alone blast and perl to generate data.