Detecting non-exonic conserved regions

Question

[IP]

Hi!

I am trying to detect conservation in non exonic regions of the human genome. What I have is is a bed file obtained from the UCSC genome browser Cons Indels MmCf Track. This track shows conserved regions in the genome. When I displayed the file in the genome browser, I can see that there are regions showing a lot of tracks within specific regions that are non exonic. What I would like to do is to convert this bed file with the tracks to a x,y signal and then run a signal detection algorithm on it to detect those conserved regions.

I have an idea about the signal detection algorithm I am going to run, but I am not sure about how to go from a bed file to a x,y signal. Does anyone have an idea?

Thanks a lot for it,

By the way, if you think that I am not aproaching my problem in a proper way, let me know :)

EDIT:

My bed file is a BED3 file

Answer 1

[Chirag Nepal]

You can download CNE (conserved noncoding elements) from ANCORA browser http://ancora.genereg.net/ These conserved elements are outside exons. You can download regions based on different threshold (70%conservation, 80%, 90% and so on) and also based on conserved with respect (mouse, frog or zebrafish). Download data from ANCORA and intersect with regions of your interest.