Finding motifs with Homer for obscure species.

Question

[a.rex]

I have recently done some ATAC-seq in an obscure invertebrate organism. I have a bed file for peaks that changed under different biological conditions. I have run this through Homer, giving the whole genome as background, and have obtained a list of motifs enriched under these peaks. Problem is, some of the motifs are for genes that do not exist in my organism (i.e. Arabidopsis specific, or human specific motifs).

How do people identify motifs for organisms not accounted for in the Homer database? Just blast TF against transcriptome/genome of interest?

[afli]

Hi, I haven't used homer. But you may try meme to find the motifs:http://meme-suite.org/.

Aifu.

[a.rex]

Hi - why is this better?

[afli]

Hi, because you can choose one motif database to do the motif enrichment, but I am not sure if your organism has the corresponding database, there are JASPAR, CIS-BP, FLY, WORM, and so on.

You can download the database here, http://meme-suite.org/doc/download.html. You can also transform other motif format to the meme format and do the analysis, see the detailed manual of meme.