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Phastcons score interpretaion

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
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updated by Ram Ram • written by michelle • michelle

Define highly.

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

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written by karl.stamm karl.stamm

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.

• 1 views • link
updated by Ram Ram • written by michelle • michelle

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.

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written by Chirag Nepal Chirag Nepal

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.

• 0 views • link
written by michelle • michelle

1 answer

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.

• 0 views • link
written by michelle • michelle

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