How to merge different motif files(obtained from MEME) for GOMO annotation in batch?

[xuzihe]

I have many motif files from MEME prediction. I want to annotate these motif files using GOMO in batch. I tried using " cat motiffile1 motiffile2 ...motiffilexx > mymotif" then upload the "mymotif" to GOMO website. But it seemed that only the motifs in  motiffile1 could be recognized as input motifs. Could you help me solve this problem? Thanks!

[CharlesEGrant]

Hi Xuzihe.

The MEME motif format is described here. Simply concatenating MEME files won't conform to that format. You'll have to hand edit the files so they match the prescribed format.

Alternatively if you download and install a local copy of the MEME Suite, it includes a utility for merging MEME files: meme2meme.

Charles

  

[xuzihe]

 According to your kind suggestion, I have got a merging MEME file using meme2meme. But how to  build  a corresponding relation between motifs in the new merged file and  those in my original files?

[James Johnson]

In answer to your second question. Unless you specify "-numbers" and/or "-consensus" when running meme2meme the output motifs will have the same identifiers as the input motifs. If there are multiple motifs with the same identifier then they will have ".X" appended where X is a number. This number will normally start at 1 and increase for every motif with the same name found.

Alternatively you could specify "-numbers" and the motifs would be numbered based on the order they appeared in the files.