[Genome] A question about conservation score

[Brooke Rhead]

Hello Shan,

There is not an easy way to calculate conservation scores from a subset 
of species in the multiple alignment.

However, you might be interested in our new 28-way Conservation track on 
the hg18 browser (even though it is human-based, not mouse-based). There 
are two separate conservation scores calculated there: one for all 28 
vertebrates in the 28-way alignment, and one for only the 10 placental 
mammals in the alignmnent.

I hope you find this information useful.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group


Shan Yang wrote:
> Hi,
> I want to get the conservation score for mouse against available 
> mammals. I can see there is a file called 
> "<http://hgdownload.cse.ucsc.edu/goldenPath/mm8/phastCons17Scores/>Conservation 
> scores for alignments of 16 vertebrate genomes with Mouse" on the 
> download page. Is there a way of calculating conservation score with 
> less species (e.g. only mammals)?
> 
> Thank you very much!
> 
> Shan
> 
> Shan Yang, PhD
> Genome Biology Division, L-452
> Chemistry,  Materials & Life Sciences Directorate (CMLS)
> Lawrence Livermore National Laboratory
> 7000 East Ave, Livermore, CA, 94550
> 
> Ph:  925-422-7389
> Fax: 925-422-2099
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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