Hello Anneke, Here is a previously-answered mailing list question that describes how to see data from Mouse Retrovirus Tagged Cancer Gene Database (RTCGD) in the Genome Browser:
http://www.soe.ucsc.edu/pipermail/genome/2006-May/010551.html Note, however, that the RTCGD has updated their links for the latest mouse browser, mm9 (July 2007): http://rtcgd.abcc.ncifcrf.gov/mm9/easy_search.html If you have further questions about the RTCGD site, I suggest contacting them at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 02/13/09 01:12, Lehmann, Anneke wrote: > Hello Brooke, > thanks a lot for your email! I am using BLAT located at > http://genome.ucsc.edu/cgi-bin/hgBlat > and I can see my sequence and the reference gene side-by-side. > The only information I am missing is the information where other scientists > did find there retrovirus integrated into the genome (maybe next to my BLAST > sequence). > So I need to see the retrovirus tagged cancer gene information to compare my > sequence with them. > > I hope you can help me out. > I whish you a nice weekend, > Anneke > > > -----Ursprüngliche Nachricht----- > Von: Brooke Rhead [mailto:[email protected]] > Gesendet: Freitag, 13. Februar 2009 04:37 > An: Lehmann, Anneke > Cc: '[email protected]' > Betreff: Re: [Genome] Question aubout retroviral tagged cancer genes > > Hello Anneke, > > Can you provide some more information? Are you using BLAT, located here?: > > http://genome.ucsc.edu/cgi-bin/hgBlat > > If so, when you BLAT a sequence, set the output type to "hyperlink". > Then, after hitting submit, there will be "browser" links to view a > graphical representation of your sequence in the Genome Browser, and > "details" links to see your sequence and the reference sequence > side-by-side. > > Also see this free online tutorial: > http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml > (Look under "UCSC Introductory Genome Browser Training".) > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 02/12/09 07:44, Lehmann, Anneke wrote: >> Dear UCSC Genome Browser Team, >> >> I habe got a question concerning the display of common integration sites >> found in different genes. >> I cannot find the button I have to use to display my sequence I did blast, >> the reference genes AND the RTCG. >> Could you help me please?! >> Thanks a lot, Anneke Lehmann >> Anneke Nina Lehmann >> Abteilung Molekulare Pathologie >> Heinrich-Pette-Institut >> Martinistraße 52 >> 20251 Hamburg >> Tel: 49-40-48051-274 >> Fax: 49-40-48051-187 >> email: >> [email protected]<mailto:[email protected]> >> homepage: www.hpi-hamburg.de >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
