Hi Maria, The data is generated from the RefGenes track. The track description describes the process, but in short: sequences are picked up from GenBank daily releases, aligned to the genomes using BLAT, and incorporated into the GenBank sourced tracks each evening (excluding Sundays).
The sequence content of all GenBank tracks is independent of full GenBank build releases ( ex: RefSeq Release 41, GenBank Release 161.0 ). The alignments are also independent of those you can obtain at Entrez. The individual sequence data is versioned in the track's linked tables ( ex: NM_XXXXX.XX, NP_XXXXX.X ), but we do not usually capture this information when derivative tracks are created. If we should start doing this is under discussion. We can tell you that the track was completed on Nov 3rd. 2009. Meaning, any sequences initially released or updated since that date were not included. You might be able to use this information to reconstruct a rough view of what the track looked like in early November last year. Please let us know if we can help more, Jen UCSC Genome Browser Support On 7/16/10 1:30 PM, Xin Ma wrote: > Hi Jen, > > Thanks for the quick reply. I am actually looking for the file > generating description for the refGene file in particular on > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/. > This file is not just a refgene annotation, but restricted to the cds > region only. Therefore, I need to know which version of the annotation > it has used when they created this file. Furthermore, I do see some > differentiation between the cds region in this file and the annotation > file in the hg19 annotation dataset. So it's very important for me to > know which kind of filters it has been applied to. > > Best, > Maria > > On Fri, Jul 16, 2010 at 1:19 PM, Jennifer Jackson <[email protected] > <mailto:[email protected]>> wrote: > > Hello Maria, > > This type of information can be found on the track's description > page. To view this, open the assembly browser to the target database > and click on the track name. > > For hg19, the path would be: > 1 - http://genome.ucsc.edu/ > 2 - Genome Browser > 3 - Choose Clade = Mammal, Genome = Human, Assembly = Feb. 2009 > (GRCh37/hg19) and submit > 4 - RefSeq Genes is in the third track grouping, Gene and Gene > Predictions > > I hope this information is helpful. Please feel free to contact the > help mailing list again if you require further assistance. > > Best regards, > > Jen > UCSC Genome Browser Support > > > On 7/16/10 1:13 PM, Xin Ma wrote: > > Hi, > > I am trying to use the refGene file on > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/alignments/, > however I can't really find corresponding information about this > file on how > this file was created, which version of the gene annotation file > it has used > and what kind of filters, if any, have been applied when > generating this > file. > Please direct me to the right place if you know where I can > find these > information. > > Thanks, > Maria > _______________________________________________ > Genome maillist - [email protected] > <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
