from coordinate to motif

Question

[Shuang He]

Hi, 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!

[Prakash]

There are several, that perform motif analysis. on genomic regions

HOMER MEME ChIPSeek

Answer 1

[ATpoint]

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.

Answer 2

[Alex Reynolds]

You could make your own database with FIMO and query it as needed:

https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491

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

Or:

$ 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.