Finding motifs for TFs binding sites in my sequences

Question

[R.Blues]

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.

Answer 1

[Santosh Anand]

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."

[R.Blues]

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! :)

[Santosh Anand]

Happy that it was helpful.

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