Question: Phastcons score interpretaion
gravatar for michelle
4.8 years ago by
michelle10 wrote:

Hey All,

I obtained my PhastCons scores from USCS browser and sum scores for individual sites together. I was wondering if I average the sums by length, in what range (or a cutoff) it means my DNA element is highly conserved.  

Thank you :)



alignment • 2.6k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by michelle10

Define highly.

Maybe look at a gene you consider highly conserved and measure it by the same method.

ADD REPLYlink written 4.8 years ago by karl.stamm3.8k

It is an enhancer element I found in mice. I want to see whether it is conserved across species. Should I use the average score? If so, like what is the cutoff for conservation.

ADD REPLYlink modified 10 months ago by RamRS30k • written 4.8 years ago by michelle10

PhastCons scores range between 0-1. So the score for any nucleotide varies from 0-1. You can sum the score for the length of your region and divide by the length to get the score between 0-1.

ADD REPLYlink written 4.8 years ago by Chirag Nepal2.2k

I did! But I was just wondering whether there is a cut off for conservation. How do I interpret my average score? In what range, it means it is definitely not conserved.

ADD REPLYlink written 4.8 years ago by michelle10
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