Regulatory motif analysis in Integrated Genome Browser

Question

[nkmullin]

I am trying to locate specific regulatory motifs near the start sites of custom tracks I have in IGB. Is there a way to do this in the program? I thought I might be able to find tracks for certain families of TF binding sites, but have had no luck.

I have used oPOSSUM 3.0 for this in the past, but wanted to try and keep all analysis in IGB this time.

Thanks in advance!

Answer 1

[Nowlan Freese]

Hi nkm34,

The first thing that comes to mind would be to use the Advanced Search function in IGB to search for your specific motifs.

1. Click on the Advanced Search tab.
2. Select Residues under the Search dropdown menu.
3. Enter your motif(s) - we support use of regular expressions and wild cards, and you can input multiple motifs simultaneously by separating them with the pipe symbol.
4. Click on the magnifying glass to search.

You can find more information in the User's Guide - https://wiki.transvar.org/display/igbman/Advanced+Search

Nowlan

[nkmullin]

Thanks so much Nowlan. This is quite helpful. I'm still getting acquainted with IGB in general.

Nate