How can I locate motif in DNA sequence.

Question

[Rashedul Islam]

I my ChIP-seq data, I used HOMER to call motifs. Now I have few regions of interest and I want to look at the DNA sequence which motifs are present. Any suggestion of tools how can I do this?

I attached the following example from M. R. Mansour et al., Science (80). 346 (2014) to show what I want to generate. Thanks!

Motifs located in the DNA sequence

[ATpoint]

FIMO from MEME suite is an option. Load in your regions and filter for the motifs that popped up in Homer.

Answer 1

[Hussain Ather]

You could visualize the regions of interest in IGV or UCSC Genome Browser

[Ian]

If you use the UCSC browser you can enable the Public Trackhub 'JASPAR 2018 TFBS', which is good for the following genomes: hg19, hg38, ce10, dm6, sacCer3, and araTha1.

You can enter the coordinates of your sites of interest as Custom Tracks, as BED formated genome coordinates.

Answer 2

[Rashedul Islam]

I found this tool (CIS-BP) that helps to do the job. Thanks all for your valuable suggestions.

http://cisbp.ccbr.utoronto.ca/TFTools.php