Refreshing this in 2019:
fimo is not the choice here as it scans individual sequences for motif occurrence. You want to match motifs to a database, which is why
tomtom from the MEME-suite is the choice here:
tomtom [options] <query motif file> <target motif file>+
<query motif file> is a motif file in MEME format and the
<target motif file>+ are known motif file to compare your motifs against. This can be obtained e.g. from the download sections of HOCOMOCO or JASPAR. Both provide them in MEME format already. In case of JASPAR you can download the individial motif files and simply concatenate them using
cat into one big motif file.
tomtom will then spill out all motifs that significantly resemble your
<query motif file>. You might want to lower the default significance threshold from
tomtom to be a bit more stringent than the default of 0.5. Output Uamong others) is a html file with the results that can be opened conveniently in any web browser.
modified 3 months ago
3 months ago by
ATpoint ♦ 24k