from coordinate to motif
Does anyone know if there exists such a database who can return the possible motifs when I input the coordinate(chr,start,end)?
Thank you in advance!
For individual motifs, I prefer
fimo from the MEME suite. It accepts fasta format.
Bedtools getfasta can convert coordinates to fasta. Motif PFMs can be downloaded from JASPAR.
You could make your own database with FIMO and query it as needed:
Once you have such a resource, it is easy to query on an ad-hoc basis:
$ echo -e "chrN\t1234\t5678" | bedmap --echo --echo-map --delim '\t' - fimoResults.bed > answer.bed
$ bedmap --echo --echo-map --delim '\t' myRegions.bed fimoResults.bed > answer.bed
FIMO results generally include the sequence of the TF model, but you can export to
samtools faidx for getting back specific sequence over the wider region.
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