Question

Finding Similarities In Predicted Enhancers Of Different Genes

0

Entering edit mode

11.2 years ago

Diana ▴ 910

Hi all,

I have predicted enhancers for 6 genes. I want to compare these enhancers with each other to find a subset out of all these which are similar to each other in terms of the motifs that they have. All I find are methods that do a pairwise comparison (such as D2z) between enhancers but I don't find that informative as I want enhancers which are similar from all 6 genes. Does any one know any methods that can accomplish that? or is it possible to extract from pairwise output such as D2z the enhancers from 6 genes that are all similar to each other?

Thanks!!!

enhancer • 2.4k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 11.2 years ago by Diana ▴ 910

score 1 · Answer 1 · 2013-03-12

1

Entering edit mode

11.1 years ago

aravind ramesh ▴ 540

You may useful tools for extracting motiffs which are similar for all of the 6 sequences. YMF 3.0

STAMP

MOST

Hope this will help you.

ADD COMMENT • link 11.1 years ago by aravind ramesh ▴ 540

0

Entering edit mode

Thanks a lot aravind!

ADD REPLY • link 11.1 years ago by Diana ▴ 910

0

Entering edit mode

You can consider to Upvote, if my answer was useful to you.

ADD REPLY • link 11.1 years ago by aravind ramesh ▴ 540