[Genome] 5-way alignment

[Yu Zhou]

Hello,

I have mapped hundreds of sequences (from 10 nt to 150 nt) to the
human genome (hg18). Now, I want to see whether the mapped regions are
conservative or not only in five species
(human/mouse/rat/dog/chicken), neither in the 17-way alignment, nor in
the 28-way alignment. In other words, I need the phastCons scores for
a 5-way alignment.

My current idea is to extract the 5-way alignment from the 17-way or
28-way alignment provided by UCSC, and then delete the columns at
which all the 5 species are gaps. Is that reasonable? If so, how to
calculate the phastCons scores for the 5-way alignment? If not, could
you give me a suggestion?

Thanks a lot in advance!


-- 
Best regards,

Yu Zhou