Hi Thomas, We don't supply style sheets for the XML returned from our very basic DAS server -- could that be the problem? I can see the raw XML results of the query using FireFox. Have you tried using a DAS client tool?
In case the raw XML is what you need, attached is the result of the command "wget -O hg19_types.xml 'http://genome.ucsc.edu/cgi-bin/das/hg19/types'". (The attachment will be stripped from the email that goes out to the genome list, but should reach you Thomas.) Hope that helps, Angie ----- "Thomas Juettemann" <[email protected]> wrote: > From: "Thomas Juettemann" <[email protected]> > To: "Angie Hinrichs" <[email protected]> > Cc: "Vanessa Kirkup Swing" <[email protected]>, [email protected] > Sent: Friday, January 14, 2011 10:45:18 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Intron/Exon boundaries > > Hello Angie & Vanessa, > > thank you for your helpful reply. > > One more question, the link that I assume lists the available types > http://genome.ucsc.edu/cgi-bin/das/hg19/types > does not seem to work. I tried it on Mac using Chrome and Safari. > > Best wishes, > Thomas > > On Fri, Jan 14, 2011 at 19:05, Angie Hinrichs <[email protected]> > wrote: > > Hi Thomas, > > > > We actually do have a simple DAS server: > > > > > http://genome.ucsc.edu/cgi-bin/das/hg19/features?type=ensGene;segment=13:32889611,32973347 > > > http://genome.ucsc.edu/cgi-bin/das/hg19/features?type=knownGene;segment=13:32889611,32973347 > > > http://genome.ucsc.edu/cgi-bin/das/hg19/features?type=refGene;segment=13:32889611,32973347 > > http://genome.ucsc.edu/cgi-bin/das/hg19/types > > > > (segment=chr13 works too, but we accept "chr"-less coords for > compatibility with Ensembl) > > > > In general, our DAS server shows a simple GFF view of the data; more > complete info can be obtained by FTP (hgdownload.cse.ucsc.edu), Table > Browser, or mysql (genome-mysql.cse.ucsc.edu), especially for the UCSC > Genes (knownGene) track with many related database tables. > > > >> Also, are the genomic coordinates different between UCSC, Ensembl > and > >> NCBI? > > > > It depends on which genomic coordinates we're talking about. The > same genome assembly sequence is used by all 3: hg19 = GRCh37, > obtained from NCBI. Genomic coordinates of annotations may differ, > for example if we show Ensembl Genes from a previous release of > Ensembl, although we do regularly update those. Also, our RefSeq > Genes track is based on our own BLAT alignments of cDNA sequences > downloaded from GenBank, so there may be some small differences in > coords vs. NCBI. > > > > Hope that helps, > > Angie > > > > ----- "Vanessa Kirkup Swing" <[email protected]> wrote: > > > >> From: "Vanessa Kirkup Swing" <[email protected]> > >> To: "Thomas Juettemann" <[email protected]> > >> Cc: [email protected] > >> Sent: Thursday, January 13, 2011 2:59:03 PM GMT -08:00 US/Canada > Pacific > >> Subject: Re: [Genome] Intron/Exon boundaries > >> > >> Dear Thomas, > >> > >> For newbie questions, the archived mailing list questions are a > great > >> resource! To get to this from the home page click on "Contact", > enter > >> a search term for "Search the Genome mailing list archives:" and > click > >> on "submit". > >> > >> > >> Here is a previously answered mailing list question that should > help > >> you: > >> > >> https://lists.soe.ucsc.edu/pipermail/genome/2009-April/018677.html > >> > >> > >> Information on the hg19 (GRCh37) assembly can be found on the > gateway > >> page: > >> > >> http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19 > >> > >> The hg19(GRCh37) assembly was created by The Genome Reference > >> Consortium > >> (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/)and is > used > >> by UCSC, Ensembl and NCBI. > >> > >> > >> Hope this helps! Please contact the mailing list if you have > further > >> questions. > >> > >> Vanessa Kirkup Swing > >> UCSC Genome Bioinformatics Group > >> > >> > >> > >> ----- Original Message ----- > >> From: "Thomas Juettemann" <[email protected]> > >> To: [email protected] > >> Sent: Thursday, January 13, 2011 6:38:25 AM > >> Subject: [Genome] Intron/Exon boundaries > >> > >> Hello all, > >> > >> again one of those newbie questions. > >> > >> I was wondering if you could give me some background information > >> about > >> intron/exon boundaries. > >> I am looking for something on UCSC site that is similar to this: > >> > >> > http://www.ensembl.org/das/Homo_sapiens.GRCh37.transcript/features?segment=13:32889611,32973347 > >> > >> It seems to be possible by using the table browser, but is there > also > >> a way using DAS or via FTP? > >> > >> Also, are the genomic coordinates different between UCSC, Ensembl > and > >> NCBI? > >> > >> > >> Thank you & Happy New Year! > >> Thomas > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >
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