Great! Thanks so much for your help Vanessa and Mary. D.
On 12/17/10 5:05 PM, Vanessa Kirkup Swing wrote: > 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 (July 2007 for mm9) so I thought they might be outdated.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 found that the miRNA track on UCSC is kind of outdated compared to the 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
