Hello, The tracks containing Genbank sequence data aligned to the genomic by BLAT (ex: RefSeq, EST, mRNA) are updated weekly with the incremental releases. The NCBI build 37.1 for hg19 refers to the genomic data only. The genomic version is the name/date/source on the Gateway page for any assembly.
To check for the date a file was last updated, navigate into downloads. The date/time and size is next to the file name like this: (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/) refGene.txt.gz 10-May-2009 10:49 2.9M To check for the date a track was last updated, click into the track's description page (track name link in Assembly browser). At the end of the first section is the update info like this: (gateway -> hg18 -> RefSeq Genes) *Data last updated:* 2009-05-09 Jennifer Jackson UCSC Genome Bioinformatics Group Kwan, Phoenix wrote: > Hi Jennifer, > > Thank you for looking into this. I downloaded the RefGene file at > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/. So, the data > should come from NCBI build 37.1 as well, right? What I found is that the > Map Viewer of NCBI is still of build 36.3. So, I assume that if I look up a > gene in Entrez gene on NCBI, the data should also be of build 36.3. Am I > correct? > > Thank you very much for your help. > > Phoenix Kwan > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Friday, May 08, 2009 12:17 PM > To: Kwan, Phoenix > Cc: [email protected] > Subject: Re: [Genome] genomic locations in RefGene file > > Correction for this paragraph below. > The example data appeared to be from Entrez *NCBI Build 37.1* not *NCBI > Build 39.1* > > Jennifer Jackson wrote: > >> It appears that the data comparison in your example is between two >> different genomic assemblies. Specifically, the UCSC Browser data is >> from NCBI Build 36.1 and the Entrez data is from *NCBI Build 39.1*. <<wrong >> > > Very sorry for the confusion! > Jennifer > > >>> Kwan, Phoenix wrote: >>> >>> >>> >>>> Hi, >>>> >>>> I have found that most of the locations for the NM transcripts in the >>>> RefGene file do not match with what are in NCBI. Are the positions in the >>>> RefGene file genomic locations relative to the full length of a >>>> chromosome? Or something else? >>>> >>>> Thank you very much for your time, >>>> Phoenix Kwan >>>> >>>> _______________________________________________ >>>> 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
