Hi Ann, The table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start)is the tool that you will need to use to obtain the sequences for the DMIT loci.
While in the table browser set the following: clade: mammal genome: Mouse assembly: July 2007 (NCBI31/mm9) group: Mapping and Sequencing Tracks track: STS Markers table: stsMapMouseNew region: genome filter: click on "create". At the bottom of the page, enter the following into the Free-form query section: name like "%D%MIT%" Click "submit". output format: sequence Click "get output" Click "get sequence" This will provide you the sequences for all of the DMIT loci. If you have further questions, please email the mailing list at: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "ann eileen miller baker" <[email protected]> To: [email protected] Sent: Thursday, June 9, 2011 11:11:22 AM Subject: Re: [Genome] mouse microsatellite DMIT amplified sequences 9Je11 Sorry to be unclear: the JAX site has an old (before the mouse genome sequenced) list of DMIT amplified sequences with many "N" (can not score accurately a given base). I am trying to get the list of amplified sequences for all DMIT loci (microsatellite loci). Any leads appreciated- JAX is the natural one, but their amplified sequences are PRE-mouse genome sequencing. > Date: Wed, 8 Jun 2011 16:17:12 -0700 > From: [email protected] > To: [email protected] > CC: [email protected] > Subject: Re: [Genome] mouse microsatellite DMIT amplified sequences > > Hello Ann, > > We don't have URLs to specific sets or subsets of data, so I'm not sure > I can help you. You might try going to MGI directly: > http://www.informatics.jax.org/ and searching for the data there. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 06/05/11 16:01, ann eileen miller baker wrote: > > 5Je11 > > May I be sent the URL to access mouse DMIT amplified sequences? > > In early drafts, the file with amplified sequences also included > > (1) DMIT primer sequences > > (2) DMIT alleles of mouse inbred strains > > If those are on the same or another URL, please send that URL too. > > Thanks. > > > > _______________________________________________ > > 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
