I had to predict the effect of a few thousand SNP that we found in our re-sequencing project. I tried using ENSEMBL's tool (http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations), but it was kind of painful (it only admits 700 SNPs, takes a long time, etc.).
So I decided to write a java program (snpEff). I noticed that Galaxy does not have a tool for SNP prediction (see http://bitbucket.org/galaxy/galaxy-central/issue/156/synonymous-and-non-syno...). So I integrated snpEff it with Galaxy.
Here is a link to a tar file which includes the jar files, databases, configuration files for Galaxy, etc.
http://www.mcb.mcgill.ca/~pcingola/snpEff.tgz
YOu'll find the databases for hg37 and mm37, but I'll be happy to create and update the tool for the genome of your choice. The program first loads the database for a genome (it takes 20 secs in my computer) and then calculates the effect for all SNPs (I used an Interval-Tree structure, so it's very fast).
I hope you find it useful. Yours
Pablo Cingolani
P.S.: Needless to say, the code is open source (I'll post it on sourceforge as soon as possible). In the mean time you can download it here http://www.mcb.mcgill.ca/~pcingola/SnpEffect_eclipse_project.tgz
P.S.2: I've attached an image of a demo run in my Galaxy server
