Question: Batch Multiple Alignments by COBALT?
gravatar for noel.garber
3.2 years 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 ( 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 • 1.2k views
ADD COMMENTlink modified 3.2 years ago by h.mon31k • written 3.2 years ago by noel.garber0
gravatar for h.mon
3.2 years ago by
h.mon31k wrote:

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

ADD COMMENTlink written 3.2 years ago by h.mon31k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1225 users visited in the last hour