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How to find motif in other genes?

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

motif dna
• 3,461 views • link
written by agata88 agata88

EMBOSS fuzznuc, available on Galaxy as well

• 1 views • link
written by Asaf Asaf

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

• 1 views • link
written by GenoMax GenoMax

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

• 1 views • link
written by agata88 agata88

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.

• 1 views • link
written by GenoMax GenoMax

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?

• 1 views • link
written by agata88 agata88

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.

• 1 views • link
written by GenoMax GenoMax

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