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