Conservation score for selected species

Question

[Aishwarya Kulkarni]

I have certain RNA Binding Protein sites that I have predicted computationally and they are said to be conserved in previous literature. I want to know if there is any track/tool that gives the conservation score or flags the conserved sequence in the specific species (or just mammals).

[Ashutosh Pandey]

The two resources I can think of now:

1. GERP++ scores: http://mendel.stanford.edu/SidowLab/downloads/gerp/
2. PhastCons scores from UCSC: Here is a relevant post

[Aishwarya Kulkarni]

This is very useful information, thanks!

[Aishwarya Kulkarni]

For GERP score is -0.5334 a somewhat conserved element?

Answer 1

[Alex Reynolds]

The UCSC Genome Browser carries various conservation tracks. You can manually score your sites against them with BEDOPS, e.g.: A: Average PhastCon score for a bed file

[Aishwarya Kulkarni]

Thanks again , I will use the bedops code to calculate avg phastcon score using this track.