Find a known motif in new sequences

Question

[Diana G.]

Hi all! I have a known motif, and I am trying to find it in several sequences. How can I check whether these sequences have or not this known motif? Please be aware, I do not want a new motif, I want to check whether the sequences match (of course not perfectly but relatively close) to a certain motif.

[Diana G.]

Hi guys! I tried FIMO, as pointed out it was the easiest to use. But I also tried motifmatchr and both of them work fine. ATpoint acvill Thank you for your help!!

Best, Diana

Answer 1

[ATpoint]

FIMO does that. Input is a fasta file with sequences, and a motif file, for example from JASPAR.

Finding individual motif occurrences with FIMO from the MEME suite

Answer 2

[acvill]

As ATpoint suggested, FIMO is probably the easiest to implement. If you like R, you can try motifmatchr or findMotifs.