[BioC] How to retrieve 'conservation score' sequence?

[Sean Davis]

On Tue, Dec 16, 2008 at 2:02 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
>
> Hi,
>
> I have a list of putative transcription factor binding sites, and in
> order to continue with the most relevant ones for further analyses i
> would like to filter on 'conservation score' (the assumption is that
> conserved sequences are more likely to be functional than less/non
> conserved sequences). I have read on this, and found out that both
> ENSEMBL (GERP score) and UCSC Browser (multiz alignment) provide this
> info (although calculated using different algorithms). Moreover, in both
> genome browsers i can view the score. However, i don't know how to
> retrieve the score for a list of sequences...
>
> I was thinking/hoping that e.g. biomart could be used for this, but i
> could not find the appropriate filter. I am not familiar enough yet with
> UCSC to find a suitable way of doing this.
> Therefore, any pointer on how to best tackle this issue would be
> appreciated!

See here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons28way/

If you are in another species, you can go to that URL and find the
phastCons data.  There is information in the directory and on the UCSC
site about how these are calculated.

Hope that helps.

Sean