[Genome] 5-way alignment

[Ann Zweig]

Hello Yu,

	If you would like to determine the phastCons measurements for a set of 
species other than those we've done, you will need to download the 
phastCons package and run it yourself on the extracted subset from the 
multiple alignment.  PhastCons is available from Adam Siepel's web page: 
  http://compgen.bscb.cornell.edu/~acs/software.html

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Yu Zhou wrote:
> 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!
> 
>