Search for a certain motif in a set of promoters


I am looking of a tool in GALAXY that I can provide it with two inputs:

a) a set of promoter sequences (all with the same size) and

b) a certain motif of 10-15 nucleotides

In order to search the promoter sequences for the certain or similar motifs (different variants).

Any help will be appreciated,

Many thanks in advance,


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Hi @Manolis1

Please see the tools in the group “Motif Tools”. Galaxy EU has a few more tool options than Galaxy Main

Screenshot for EU:

Depending on how your motif was generated/formatted already, you may be able to go straight to the FIMO tool.

There are many more motif discovery/analysis tools in the ToolShed that could be installed into your own Galaxy server. Some of those are also likely hosted by other public servers. There isn’t a good way to batch search by tool against all of them (yet!), so you would just need to review to see if any of the servers have tools that meet your needs:

Others might know more about the best tool/s or public server/s to use … so more replies are welcomed.

Hi Jennifer,

Many thanks for your answer.



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Hi @Manolis1,

I have a list of promoter regions generated by promoter2 tool and a list of regions (exons, transcripts) generated by StringTie tool. I would like to know whether those identified promoter regions will fall in the second list.

I feel may be you have similar problem. I f you have found the way for your above query or know way for my query please suggest.

Thank you

Hello @YKV

I have never used the promoter2 or the StringTie tool. So I do not really know for what purposes these tools are used for. But seems to me that our problems are different.

I had a set of certain promoters and I wanted to know if a certain motif (and also variations of it) is present in them and if yes how frequent is this happening. I did solve my problem in 2x steps: a) use the database of the organism that I am working with to extract the specific promoter regions and b) by feeding these sequences then to FIMO (as one of the options suggested by Jennifer (see the answer to my initial question)).

I do not know if this helps somehow.

I am sorry but I never had a similar problem like yours to solved.



Hi @Manolis1
Thank you so much for your time. Now I got it clear. All I have is raw genome sequence(in fasta), RNA sequence(fastsanger) and no reference sequence is available. So I am trying to find out what I can do with that to annotate. I will also try in case if I can try the way you used.

Thank you