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?