Conservation score PhyloP for animals
Piero Fariselli
Dear Genome Browser's team,
I am interested in having files similar to the human phyloP100way for
other species, such as Dog, Cat etc.
Of course it would be great having the data available and updated, by
you, but I can understand the problems.
So I wonder if you can indicate me how I can obtain that using your
data, and possibly the pipeline you followed
for the human data.
Thank you in advance for your help and courtesy,
Yours faithfully,
Piero Fariselli
Chris Villarreal
Dear Piero Fariselli,
Thank you for your question about the UCSC Genome Browser. Here is the process we used to create the alignment files:
1. Generate lastz/chain/net pairwise alignments to each species for the multiple alignments. You may find it beneficial to use some of the pairwise alignments we already provide on our downloads server here: http://hgdownload.soe.ucsc.edu/downloads.html.
2. Use Multiz with those results to compute the multiple alignments. Multiz can be found here: http://www.bx.psu.edu/miller_lab/, under “Software” click Multiz and TBA alignment programs.
3. Run PhastCons, which can be downloaded here: http://compgen.cshl.edu/phast/. This is a helpful resource for using PhastCons: http://compgen.cshl.edu/phast/phastCons-HOWTO.html.
4. Run phyloP, part of the PHAST package.
Here is the latest example of the procedure for a 20-way alignment in rn6.txt:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/rn6.txt.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
-Chris V
UCSC Genome Browser
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