Hi Peter, You should be able to use the DAS server to get info for SNPs. An example query is in our FAQs here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download23
An explanation of how to find the names of Genome Browser tables is here: https://lists.soe.ucsc.edu/pipermail/genome/2012-June/029680.html Note that our SNP tracks have become four different tracks (see an explanation on the SNP track details page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp135); if you want the most inclusive track, use snp135 (assuming you are using the human hg19 assembly). We are hoping that the MySQL server will become useable again over the weekend, but it's not guaranteed. -- Brooke Rhead UCSC Genome Bioinformatics Group On 6/29/12 2:27 AM, Peter Schols wrote: > Hi Luvina, > > Thanks for the information. I have two questions: > > 1. Is there a web API for querying SNP information. Similar to e.g. > http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr2:100000,200000 > in which XML is returned, but for SNPs? > > 2. Do you have any estimate on when the MySQL server will be up and > running again? > > > Many thanks in advance for a great resource! > > Best wishes, > > Peter Schols > > > On 28 Jun 2012, at 18:31, Luvina Guruvadoo wrote: > >> Hi Peter, >> >> We are currently having hardware problems on our MySQL server and >> are working to resolve them. In the meantime, you can use our >> download server (http://hgdownload.cse.ucsc.edu/downloads.html) or >> FTP server (ftp://hgdownload.cse.ucsc.edu/goldenPath) to download >> whole tables or you can use our Table Browser >> (http://genome.ucsc.edu/cgi-bin/hgTables) to download specific >> information from the tables. If you're unfamiliar with the Table >> Browser, please see the User's Guide at >> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. If you >> still have questions about how to look up specific information, >> please let us know. >> >> Please contact us again at [email protected] if you have any >> further questions. >> >> --- Luvina Guruvadoo UCSC Genome Bioinformatics Group >> >> On 6/28/2012 2:09 AM, Peter Schols wrote: >>> Dear UCSC genomics group, >>> >>> It seems like the UCSC MySQL server is having issues with the >>> hg19 genome. Are you aware of any problems, and do you have an >>> approximate time frame in which this will be solved? >>> >>> Many thanks in advance! >>> >>> Peter Schols _______________________________________________ >>> 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
