The rtracklayer package is capable of downloading the conservation scores
from UCSC.

This is particularly easy with the devel version of rtracklayer:

> library(rtracklayer)
Loading required package: RCurl
> session <- browserSession()
> track(session, "multiz28way", GenomicRanges(10000, 20000, "chr1", "hg18"))
A UCSCData object with 1 cols on 9979 ranges in 1 sequences
trackLine: track name=Conservation description="Vertebrate Multiz Alignment
& PhastCons Conservation (28 Species)" type=wiggle_0

To get the phastCons values from 10000 to 20000 on chr1 in the human genome.

I'm working on a way to make it fast to retrieve these values for a large
number of ranges (e.g. genes).

On Tue, Dec 16, 2008 at 11:02 AM, Hooiveld, Guido <Guido.Hooiveld@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!
>
> TIA,
> Guido
>
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email:      guido.hooiveld@wur.nl
>
>
>
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