Question: Batch Multiple Alignments by COBALT?
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gravatar for noel.garber
7 months ago by
noel.garber0 wrote:

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. :)

cobalt blastp blast alignment • 362 views
ADD COMMENTlink modified 7 months ago by h.mon11k • written 7 months ago by noel.garber0
0
gravatar for h.mon
7 months ago by
h.mon11k
Brazil
h.mon11k wrote:

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

ADD COMMENTlink written 7 months ago by h.mon11k
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