Hello Yu,
Please read the following FAQ on that subject:
http://genome.ucsc.edu/FAQ/FAQdownloads#download7
And this previously-answered mail list question:
http://www.soe.ucsc.edu/pipermail/genome/2006-July/011181.html
If you are still having trouble understanding the EST data, do not
hesitate to
contact the list again.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Yuan Jian wrote:
> Hi Ann,
> Thanks.
> in your data set "all_est", is there a way to know whether an EST is
> 5'EST or 3'EST?
>
> YU
>
>
> --- On *Wed, 19/11/08, Ann Zweig /<[EMAIL PROTECTED]>/* wrote:
>
> From: Ann Zweig <[EMAIL PROTECTED]>
> Subject: Re: [Genome] EST
> To: [EMAIL PROTECTED]
> Cc: [email protected]
> Received: Wednesday, 19 November, 2008, 5:23 PM
>
> Hello Yu,
>
> To create the EST annotation track, human ESTs from GenBank were aligned
> against the genome using BLAT. We simply take the ESTs that are
> deposited into
> GenBank and attempt to align them to the genome. If they align and pass
> our
> filtering standards (only alignments having a base identity level within
> 0.5% of
> the best and at least 96% base identity with the genomic sequence), then
> we
> display them in the annotation track.
>
> If you are interested in this particular EST, you may want to take a
> look at
> the GenBank entry at NCBI:
>
>
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?tool=portal&db=nucest&term=DB034871&query_key=1&dopt=gb&dispmax=20&page=1&qty=1&WebEnv=1n_JmaxR4pdhfdof_c73a6mxVAWxiRb6djnspa-kMjw79KBBGIZkqABxPzJbQb8y17U-kxsJAmn2sABGym0ZBIpQH%40263F07C28FE2FD40_0067SID&WebEnvRq=1
>
> You could contact the authors or submitters, or read their paper to
> learn more
> about this type of EST:
> http://www.ncbi.nlm.nih.gov/pubmed/16344560?dopt=Abstract
>
> Diversification of Transcriptional Modulation: Large-scale Identification
> and
> Characterization of Putative Alternative Promoters of Human Genes
>
> I hope this information is helpful to you.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
> Please feel free to search the Genome mailing list archives by visiting
> our
> home page, clicking on "Contact Us", then typing a word or phrase into
> the search box. On that same page
> (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome
> mailing
> list.
>
>
> Yuan Jian wrote:
> > if an 5'EST was in any position of exon or UTR, it is understandable
> (as you said 5' ESTs may end at any point within the transcript) . but now
> the EST of DB034871 is out of the transcript, (it is in intergene).
> > I can not understand why it can be caught by EST primers.
> > thanks
> > YU
> >
> >
> > --- On Tue, 18/11/08, Brooke Rhead <[EMAIL PROTECTED]> wrote:
> >
> > From: Brooke Rhead <[EMAIL PROTECTED]>
> > Subject: Re: [Genome] EST
> > To: [EMAIL PROTECTED]
> > Cc: [email protected]
> > Received: Tuesday, 18 November, 2008, 10:33 PM
> >
> > Hello Yu,
> >
> > See the Methods section of the description page for the EST track for an
> > explanation of what may be happening. In particular:
> >
> > "In general, the 3' ESTs mark the end of transcription reasonably
> > well, but the 5' ESTs may end at any point within the transcript. Some
> of
> > the newer cap-selected libraries cover transcription start reasonably
> well.
> > Before the cap-selection techniques emerged, some projects used random
> rather
> > than poly-A priming in an attempt to retrieve sequence distant from the
> 3'
> > end. These projects were successful at this, but as a side effect also
> deposited
> > sequences from unprocessed mRNA and perhaps even genomic sequences into
> the EST
> > databases. Even outside of the random-primed projects, there is a degree
> of
> > non-mRNA contamination. Because of this, a single unspliced EST should
> be
> viewed
> > with considerable skepticism."
> >
> > DB034871 appears to be a 5' EST.
> >
> > Additionally, here is a paper that looks helpful for explaining the
> quality of
> > EST data:
> >
> > Nagaraj SH, Gasser RB, Ranganathan S. A hitchhiker's guide to
> expressed
> > sequence tag (EST) analysis. Brief Bioinform. 2007 Jan;8(1):6-21. Epub
> 2006 May
> > 23.
> > http://bib.oxfordjournals.org/cgi/content/abstract/8/1/6
> >
> > I hope this is helpful.
> >
> > --
> > Brooke Rhead
> > UCSC Genome Bioinformatics Group
> >
> >
> > On 11/16/08 23:43, Yuan Jian wrote:
> >> Dear UCSC,
> >> I downloaded human EST from UCSC. EST is from CDNA. it means all ESTs
> > should belong to genes.
> >> but from the data I downloaded why some EST regions are neither from
> exon
> > nor from UTR?
> >> for example EST:DB034871 has 8 blocks.
> >> block 1-6 belong to no genes.
> >> thanks
> >> YU
> >>
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