Can I Infer Conservation Scores For 7-Way Alignments With Horse Using Pairwise Alignments On Ucsc?

Question

[dustar1986]

Hi,

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.

Answer 1

[Asaf]

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).