# Search for a certain motif in a set of promoters **URL:** \ **Category:** usegalaxy.org support\ **Created:** [November 22, 2019, 12:46pm UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518 "2019-11-22T12:46:16Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Manolis1](https://avatars.discourse-cdn.com/v4/letter/m/977dab/32.png) [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Post date:** [November 22, 2019, 12:46pm UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/1 "2019-11-22T12:46:17Z")
Hello, 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, Manolis ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [November 23, 2019, 3:21am UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/2 "2019-11-23T03:21:31Z")
Hi @Manolis1 Please see the tools in the group “Motif Tools”. Galaxy EU [https://usegalaxy.eu](https://usegalaxy.eu) has a few more tool options than Galaxy Main [https://usegalaxy.org](https://usegalaxy.org). Screenshot for EU: ![motif-tools-usegalaxy-eu](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/11014eb783d40e5bb5c36b76a19f87128480fa55.png) 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](http://usegalaxy.org/toolshed) that could be installed into your [own Galaxy server](https://help.galaxyproject.org/t/example-step-by-step-for-a-basic-local-galaxy-install-with-an-admin-account-created/1451/2). 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: [https://galaxyproject.org/use/](https://galaxyproject.org/use/) Others might know more about the best tool/s or public server/s to use … so more replies are welcomed. ---
**Author:** ![Manolis1](https://avatars.discourse-cdn.com/v4/letter/m/977dab/32.png) [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Post date:** [November 25, 2019, 9:11am UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/3 "2019-11-25T09:11:54Z")
Hi Jennifer, Many thanks for your answer. Best, Manolis ---
**Author:** ![YKV](https://avatars.discourse-cdn.com/v4/letter/y/9fc348/32.png) [@YKV](https://help.galaxyproject.org/u/YKV)\ **Post date:** [February 12, 2020, 1:25pm UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/4 "2020-02-12T13:25:54Z")
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 ---
**Author:** ![Manolis1](https://avatars.discourse-cdn.com/v4/letter/m/977dab/32.png) [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Post date:** [February 13, 2020, 2:17pm UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/5 "2020-02-13T14:17:47Z")
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. Greetings, Manolis ---
**Author:** ![YKV](https://avatars.discourse-cdn.com/v4/letter/y/9fc348/32.png) [@YKV](https://help.galaxyproject.org/u/YKV)\ **Post date:** [February 14, 2020, 4:46am UTC](https://help.galaxyproject.org/t/search-for-a-certain-motif-in-a-set-of-promoters/2518/6 "2020-02-14T04:46:06Z")
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 YKV