Hi there! I need some help figuring out how to do separate multiple alignments in batch. I'm new to BLAST, etc., and so far, I've been using COBALT (https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi) to test a given protein against my sequence of interest (14 residues) to find the closest match, which I then copy to Excel to do some of my own algorithms on.
The problem is that I have a list of 350 proteins to do this for, and that's going to take a really long time. I can't just paste them all into COBALT, as the algorithm COBALT uses is iterative. What I need is something that will check one protein against my specified sequence, copy the 14 closest matching residues to a list, and then repeat for the next protein, etc. Can this be done in local BLAST?
Any advice is much appreciated. :)