Hi all,
I'm trying to analyze fragments generated from in silico digests of two draft genomes to determine how many of the fragments differ between the two species. For input, I have two unordered lists of ~5,000 ~300bp fragments (one from each species); I would like to determine how many of them are identical, how many differ by 1 base, 2, 3, etc., and how many don't have a corresponding fragment in the other genome.
Is this possible? What approach should I take? I can't seem to figure out if pairwise aligners will handle unordered lists like this, or if multiple alignment is what I need, or if I just want to map both sets back to one of the reference genomes. I'm not very experienced at this but I'd like to learn.
Thanks,
Joanna
Thank you! That ended up working really well, and the output was super-easy to parse. Thanks so much!
Glad to here that! Please remember to upvote my (and any other) answers that you find helpful ;-)
Thanks! Always good to learn the etiquette of new online communities :D