I Am Trying To Run Fimo From Meme Suite

Question

[k.nirmalraman]

I am trying to use FIMO from MEME Suite.

This requires the motif that we are trying to identify in a specific format as mentioned here.

Is there any script in meme suite that does this based on the motif sequences at hand?

Thanks a lot!

[tolsma.joseph]

The comments below are good advice. FIMO also has an in-browser function where you can just type in your motifs. It's pretty intuitive and allows you to build the matrices visually. iupac2meme works for converting but I would recommend getting comfortable moving things into MEME format as there are many useful tools in MEME.

I believe HOMER has an option for getting output in MEME format.

Answer 1

[raunakms]

If I get it right, u have bunch of sequences and predict motifs based on your sequences. If so directly use MEME http://meme.nbcr.net/meme/cgi-bin/meme.cgi instead of FIMO !!!

[k.nirmalraman]

In FIMO u generally look for a motif that you are interested in and MEME gives u random motifs... Also, MEME does not scale for large data sets...

Answer 2

[charlesegrant]

FIMO and MEME do two different things. MEME performs de novo motif discovery. FIMO searches for matches to given motifs. When using MEME you typically don't know what the motif is, but you have a set of sequences many of which you suspect contain instances of the motif. MEME will scan those sequences, find short subsequences that are statistically overrepresented, then align those subsequences to identify candidate motifs. The output of MEME is a position specific frequency matrix (PSFM). The PSFM models a motif as an array of letter frequencies for each position in the motif. Once you have PSFM for the candidate motifs from MEME or some other source you can then use FIMO to look for matches to the candidate motifs in arbitrarily large sequence sets.

If you have sequences for instances of the motif you can run MEME on just those sequences. This should generate the motif PSFM that FIMO needs. Alternatively, you can align the motif sequences yourself, count the letters at each position, and record that as a matrix of letter counts. MEME Suite provides several scripts for translating several popular count matrix formats into the MEME PSFM format. These scripts are all listed in the MEME documentation in the section titled "File Format Conversion Utilities". As Poe mentions, if all you have is a consensus sequence, you can use iupac2meme to convert a simple consensus sequence to it's equivalent representation as position specific frequency matrix.

Answer 3

[PoGibas]

Yes, MEME suite has iupac2meme that will do what you want.