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Batch Multiple Alignments by COBALT?

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. :)

blast blastp cobalt alignment
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updated by h.mon h.mon • written by noel.garber • noel.garber

1 answer

Did you see you can download Cobalt and run it locally?

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written by h.mon h.mon

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