PhastCons score and LOD
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7.2 years ago
lomolith • 0

Hi everyone. I have a question during I trying to understand phastCons output. Can anybody explain me what different between phastCon's conservation score and LOD?

I searched almost everywhere include the paper but everything I could found is the score is "base by base conservation score" and the LOD is "log odd ratio for predicted elements"

What does it mean exactly? Is LOD transformed phastcon score or different value?

 

phastcons conservation score • 4.4k views
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7.2 years ago
Manvendra Singh ★ 2.2k

NO,

Phastcons Identify conserved elements or produce conservation scores, given a multiple alignment , you get out put in wig format a value varying from 0 to 1,on the scale that how conserved every base is by some phylotree models
   LOD score is a statistical estimate of whether two genes, or a gene and a disease gene, are likely to be located near each other on a chromosome and are therefore likely to be inherited.

calculates linkage distance, log of probability that sequences are propagating together through the generations, or how whether given genes are are in linkage (LD), it does log2 transformation of ratio between probability of some linkage value and probability with no linkage value

 

HTH

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