Entering edit mode
7.6 years ago
agata88
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870
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
EMBOSS fuzznuc, available on Galaxy as well
+1 for fuzznuc. You would need to get upstream sequences from genes you want to test in the related organisms.
What if I am looking in whole genomes? Is it possible to run it on for example ensembl plant database?
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.
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?
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.
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!