 
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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