Hi Xu, if you can get your data into a format that Ensembl accepts (keep only lines that start with "chr", then remove the string "chr") and you're on the same assembly, then you can use the SNP effect predictor of Ensembl: http://www.ensembl.org/Rattus_norvegicus/UserData/UploadVariations
cheers Max -- Maximilian Haussler Office:+44 161 27 55980 Mob: +44 7574 246 789 http://www.manchester.ac.uk/research/maximilian.haussler/ On Wed, Jan 5, 2011 at 2:02 AM, Brooke Rhead <[email protected]> wrote: > Hi Young, > > You may be interested in our new "Personal Genome SNP format" custom > track type: > http://genome.ucsc.edu/FAQ/FAQformat.html#format10 > It computes amino acid changes on the fly when you view items in the > Genome Browser. > > However, there's not a way to get this information out of the Genome > Browser in batch. Here's a previously-answered mailing list question on > computing amino acid changes yourself: > https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019496.html > > I hope this is helpful. If you have further questions, please feel free > to contact us again at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/03/11 14:54, Yang Xu wrote: >> Hello, >> >> We identified SNPs on rat genome. Some of them are in coding region. Is >> there efficient way that we could find the correspondent protein mutation >> from the SNPs. >> >> For example, a SNP in Chr13: 45,220,701. How could I find out the position >> and amino acid change to that SNP? We have thousands of such kind of data. >> So we need to know the how to do that in batch. >> >> Thank you very much. >> >> Young >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
