Hi Duke, The dates next to the names are the dates when the the assemblies were released. The mm9 assembly was released July 2007. All the tracks within the assembly are based on the sequence of that assembly and can have varying dates as to when they are released or updated based on the sequence. A good way to determine when the track was last updated and the frequency it is updated is to look at the track description page.
Here is the link to the miRNA track for mm9: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr12&g=miRNA As you can see: Data last updated: 2009-06-11 whereas the Mouse mRNA track for mm9 which is updated more frequently: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr12&g=mrna Data last updated: 2010-12-13 Hope this helps clarify things for you. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Duke" <[email protected]> To: "Mary Goldman" <[email protected]> Cc: [email protected] Sent: Friday, December 17, 2010 1:22:20 PM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] most updated mRNA database? Hi Mary, Sorry for my late response, I have been too busy. Anyway, I dont have any resource for that. I was going to genome browser to use Table to download the mRNA track (http://genome.ucsc.edu/cgi-bin/hgTables?command=start) and as you can see there are three assemblies for mouse (mm9, mm8, mm7) with the date (July 2007 for mm9) so I thought they might be outdated. But based on your email, the assembly (July 2007) is just a name, but the data (and the track itself) is updated regularly? Also it looks to me that only mRNA, RefSeq, and EST data are updated regularly based on the FAQ. Does this apply to miRNA track and non-coding tracks as well? I remember when I was working with miRNA, I found that the miRNA track on UCSC is kind of outdated compared to the one on mirBase. Please correct me if I am wrong. By the way, thank you very much for your information about the mRNA data. It is very helpful for me. Thanks, D. On 12/15/10 4:56 PM, Mary Goldman wrote: > Hi Duke, > > I'm unsure of where you got the information that our most updated > version is from 2007 as our mRNA track from GenBank is incrementally > updated on a daily basis (see this FAQ for more information: > http://genome.ucsc.edu/FAQ/FAQreleases.html#release6). Can you please > let me know where you saw this? > > Note that the mRNA table contains only the mRNAs that were aligned to > the genome using BLAT. The full set of unaligned sequences can be > found here: > http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/mrna.fa.gz. > > Also, it may be of interest to you to know that you can download > copies of any of our tables here > (http://hgdownload.cse.ucsc.edu/downloads.html), which is faster than > downloading it through the table browser. Just click on your organism > of interest and then click the "Annotation database" link. This will > take you to a folder with text files of all of our tables. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > > On 12/15/10 12:50 PM, Duke wrote: >> Hi all, >> >> I am about to work with a mouse mRNA dataset, and I wonder if anybody >> knows a good (most updated, complete list) resource of mRNA? I know that >> I can use Table Browser to get the mRNA tracks from UCSC, but I think >> this one is kind of out-of-date (most updated version is mm9 in 2007). >> >> Thanks, >> >> D. >> _______________________________________________ >> 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
