Motif prediction in Bacteria species using HOMER [Chip-seq]

Question

[anu014]

Hello Biostars!

I've been going through HOMER for prediction of motifs in bacterial species such as Mycobacterium tuberculosis. I saw that HOMER doesn't have background database for any bacterial species:

Organism    Mset
human   vertebrates
mouse   vertebrates
rat vertebrates
frog    vertebrates
zebrafish   vertebrates
fly insects
worm    worms
yeast   yeast
arabidopsis plants

How to restrict the prediction for just bacterial species, so that HOMER result doesn't show motifs from other species?There's a '-bg' parameter in which we can give BED file for background. If I give Mycobacterium tuberculosis's GFF in '-bg' parameter, it will be biasing results just towards Mycobacterium tuberculosis itself.

Link - http://homer.ucsd.edu/homer/ngs/peakMotifs.html Please help. Thanks in advance.. :)

[GouthamAtla]

Just to clarify, the background sequences can be from MT itself. Ideally, the background sequences are the ones with similar characteristics of your peaks of interest.

For example, if you want to look for a motif in promoters of specific groups of genes ( lets say DE genes ) , the ideal background sequences would be the promoters from other genes that has similar expression levels and may be share same nucleotide content but are not differentially expressed.

If someone is looking at differential enhancer peaks, the background can be enhancers of similar strength but which are not differentially regulated.