I'm currently working in a model for differentiating some kinds of SNPs according to genomic signatures presen is their contexts. One of the such signatures is wether the genomic context is conserved among primates (Pan, Pongo, Gorilla, etc).

There are many kinds of different conservation measures, so I was wondering wich would be the best and wich are easily obtainable or easily available in databases for some preliminary tests. I have to acces conservation measures for small sequences (less than 100 nt) neighboring about human 50,000 SNPs, that is, when homologous sequences are available in one or more primates.

So any suggestions?