Question

Finding Similarities In Predicted Enhancers Of Different Genes

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11.7 years ago

Diana ▴ 930

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 • 2.5k views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 11.7 years ago by Diana ▴ 930

score 1 · Answer 1 · 2013-03-12

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11.7 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 11.7 years ago by aravind ramesh ▴ 540

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Thanks a lot aravind!

ADD REPLY • link 11.7 years ago by Diana ▴ 930

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

ADD REPLY • link 11.7 years ago by aravind ramesh ▴ 540