Question: how to map a motif in a series of sequences?
gravatar for haris.zafr
10 days ago by
haris.zafr0 wrote:

Hi everyone,

I have about 700 sequences of COI gene and I would like to see a certain motif that I also already have, if and if yes, where it hits in each of them. What approaches and tools could I use?

Thank you very much!!

gene • 140 views
ADD COMMENTlink written 10 days ago by haris.zafr0

What is your motif? Amino acids? DNA? Any redunant/ambiguous characters?

ADD REPLYlink written 10 days ago by jrj.healey2.9k

It is DNA and we have ambiguous characters. Thanks again!! :)

ADD REPLYlink written 10 days ago by haris.zafr0

The easiest way to do it I would think would be to create a multiple sequence alignment of all of the genes and the motif of interest. If the sequences are too long for this (MSA scales pretty horribly), you may want to consider HMM approaches, or simply making a BLAST database of your 700 sequences and querying your motif against them all - I think BLAST tolerates certain ambiguous characters but I think you're going to have to give us a bit more information to get any further (some example data for instance).

ADD REPLYlink written 9 days ago by jrj.healey2.9k
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