Question: Can I Infer Conservation Scores For 7-Way Alignments With Horse Using Pairwise Alignments On Ucsc?
gravatar for dustar1986
8.0 years ago by
dustar1986330 wrote:


I'm quite new in phylogenetics.

UCSC supplies "Conservation scores for alignments of 46 vertebrate genomes with human" in its download database.

For for some species like horse, such data is not given. However, it gives pairwise alignments comparing 7 other vertebrate genomes with horse one by one.

I wonder if I can use such data to create "Conservation scores for alignments of 7 vertebrate genomes with horse".

What is the process to achieve this?

Thanks a lot.

conservation • 1.8k views
ADD COMMENTlink modified 8.0 years ago by Giovanni M Dall'Olio27k • written 8.0 years ago by dustar1986330
gravatar for Asaf
8.0 years ago by
Asaf8.5k wrote:

You can try PHASTCons and get a conservation score (used by the UCSC genome browser) or rate4site that will use phylogenetic data to compute the evolutionary rate of each position (originally written for proteins but can use a DNA model).

ADD COMMENTlink written 8.0 years ago by Asaf8.5k
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