Question: How to find motif in other genes?
0
gravatar for agata88
3.1 years ago by
agata88790
Poland
agata88790 wrote:

Hi all!

I have 10nc sequence which represents new motif in promotor sequence of gene A. Now I would like to find this motif in other related organisms.

Any suggestion how can I do that?

Thanks in advance,

Agata

dna motif • 1.3k views
ADD COMMENTlink written 3.1 years ago by agata88790
2

EMBOSS fuzznuc, available on Galaxy as well

ADD REPLYlink written 3.1 years ago by Asaf6.1k

+1 for fuzznuc. You would need to get upstream sequences from genes you want to test in the related organisms.

ADD REPLYlink written 3.1 years ago by genomax71k

What if I am looking in whole genomes? Is it possible to run it on for example ensembl plant database?

ADD REPLYlink written 3.1 years ago by agata88790

You could look but with a 10 bp query (even before you allow mismatches) you may get a ton of hits and would still need to weed through those.

ADD REPLYlink written 3.1 years ago by genomax71k

hmm ... so this tool is not very useful in my case... unless I will prepare template by myself, which will be very time consuming... find the homology of gene, then the promotor sequence and then compare motifs. Hmm...any other idea?

ADD REPLYlink written 3.1 years ago by agata88790

You asked for a tool that can identify a 10 nc sequence in other sequences and fuzznuc will do that. Pre-computing all motif sequences (even at fixed 10 bp) is a major computational task for entire plant database, as you just realized yourself.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax71k

Ok, I found PlantProm for only promotor sequences :) http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

I past it in case somebody will have the same little problem as me :) And I will use fuzznuc. Thanks for your help!

ADD REPLYlink written 3.1 years ago by agata88790
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