Question: Finding motifs for TFs binding sites in my sequences
gravatar for R.Blues
2.3 years ago by
R.Blues80 wrote:

Hello everyone,

This is a variation of the typical question of "How can I find common motifs in my sequences?", that is usually answered by using MEME Suite.

In this case, I have 4 DNA candidate sequences (all of the same length), and I am interested in finding any possible TF binding site motif that may be in them. These sequences are all independent, so I am not interested in finding anything in common between them.

I have tried CentriMo, tool of the same suite, versus some databases such as JASPAR, but I didn't had success, and I am afraid that maybe it does not work like that, or that maybe, with these sequences, the e-value is too low for it to select a hit. Am I doing something wrong? Should I use another tool?

Thank you very much to you all.

binding sites tfs • 1.2k views
ADD COMMENTlink modified 2.3 years ago by Santosh Anand4.6k • written 2.3 years ago by R.Blues80
gravatar for Santosh Anand
2.3 years ago by
Santosh Anand4.6k
Santosh Anand4.6k wrote:

FIMO is the right tool for that

"FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences). See this Manual for more information."

ADD COMMENTlink written 2.3 years ago by Santosh Anand4.6k

Santosh, thank you very much.

At first I took a look at it, but the online tool needs the motifs to be given by the user, so (although now I realize I could have downloaded a database) I went to CentriMo. I have just installed the suite and everything went alright.

Thanks! :)

ADD REPLYlink written 2.3 years ago by R.Blues80

Happy that it was helpful.

PS: Your name reminds me of Ray Charles, of whom I am a big fan :)

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Santosh Anand4.6k
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