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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
