Hi all, I was trying to get some help here as I need to compare 2 sets of primers targeting the COI region.
I would basically like to know which primer set gives the most comprehensive diversity coverage for my target species. I'm using a general metazoan primer set (Folmer 1994) which targets 658 bp (whole COI region) and another primer set which targets a smaller region 313 bp in the COI (which should work better for my purpose). I've been trying to align the primers on Geneious to the COI species sequences downloaded from NCBI, but it looks like they don't sit in the right place for some reason. I've tried reverse complementing them and/or just reversing them, but still wouldn't target the right region. The idea then would be to BLAST the 2 different regions delimited by the 2 different primer sets and compare query coverage and species identity to see which one would work better.
Has anyone got any idea how to solve this even with a different approach in silico perhaps?