Find a known motif in new sequences
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.
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Diana G. •
2 answers
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
As ATpoint suggested, FIMO is probably the easiest to implement. If you like R, you can try motifmatchr or findMotifs.
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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