[Genome] Find conservation scores for transcripts

[Brooke Rhead]

Hello Sihui,

It is possible to retrieve conservation scores for one or two particular 
transcripts by using the Table Browser.  To do this, select the 
"phastCons*way" table from the appropriate database, then intersect that 
table with a custom track of the transcripts, and choose "data points" 
as the output.

However, because conservation score data is quite large (one data point 
for each base), the Table Browser method is impractical for more than a 
few transcripts.  Instead, you can download conservation scores for an 
entire genome (or just the chromosomes of interest), and extract scores 
for just your ranges of interest.

The phastCons score downloads are available on our downloads server:

http://hgdownload.cse.ucsc.edu/downloads.html

The phastCons file format is described here (note that position 
coordinates are 1-based, unlike most of our other data formats, which 
are 0-based):

http://genome.ucsc.edu/goldenPath/help/phastCons.html

I hope this information helps.  If you have further questions, please 
feel free to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177



szhao3 at ncsu.edu wrote:
> Hello,
> 
> Is there a fast way to get the conservation scores of a set of
> transcripts, including the intronic regions? Thanks a lot.
> 
> Sihui Zhao
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome