[Genome] gene walking & Unigene cluster mapping

[Rachel Harte]

Guoliang,

The coordinates in both the BLAT output and the database tables have
0-based starts so the first base (5' most) on a chromosome or scaffold is
position 0. For the ends, the positions are 1-based. You are correct in
saying that the BLAT output and the database table coordinates are
directly compatible in this way.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Fri, 6 Apr 2007, Guoliang Xing wrote:

> Hi Rachel,
>
>    Thank you for the info. It is what I need. The next step for me is to
> figure out which tables to query  once you release the new annotation.
>
>    What I have now is the blat result of all the probes on the affy arrays
> against Human Genome build 18.
>
>    I guess in your annotation, the gene (or exon) boundary coordinates are
>  based on genome position from 5'-most base 1 against HG 18. If this is
> the case, I can combine my BLAT results with your gene annotation info
> directly.
>
>    Then I can query my data gene-by-gene based on unique gene IDs, or do a
> "chromosome walk" from 5' to 3' and apply my statistical analysis in a
> flexible way.
>
>    Please confirm if my guess is right, and if you have additional info
> please let me know.
>
>    Thanks
>
>    Guoliang
>
> On Fri, 6 Apr 2007, Rachel Harte wrote:
>
> > Guoliang,
> >
> > Currently, we have the "Known Genes" set of genes which has not been
> > updated recently. However, within the next few days we are releasing a new
> > gene set (UCSC Genes) that will be our new gold standard for gene
> > annotation - the method for producing this gene set has changed resulting
> > in an even higher quality set of annotations which will include more
> > splice variants and also non-protein-coding genes.
> >
> > Watch out for an announcement of the release of this gene set on our home
> > page. The track control will appear in the "Genes and Gene Prediction
> > Tracks" group under the Genome Browser image. By clicking on the link above
> > this track control, you will see a description of the track and a "View
> > Table Schema" link shows the main table for this track which contains the
> > alignment information for the genes. There are other connected tables that
> > are also listed on this page.
> >
> > I hope that this helps you. Please let us know if you have further
> > questions.
> >
> > Rachel
> >
> > Rachel Harte
> > UCSC Genome Bioinformatics Group
> > http://genome.ucsc.edu
> >
> >
> > On Thu, 5 Apr 2007, Guoliang Xing wrote:
> >
> > > Dear Genome help team,
> > >
> > >     I want to code some Perl programs to compare different microarray
> > > signals on the same genes using UCSC genome browser annotation data. I'd
> > > like to download relevant gene track info in MySQL dataabse and run in
> > > local machine mode.
> > >
> > >     Let's say Affy Expression array U133 plus2 vs. Affy U95, they have
> > > different probe coverages, but some of the probes mapped to the same gene.
> > > My intuition is to map different probes on the two different arrays to a
> > > common Unigene cluster id, and then run my statistical comparison based on
> > > common cluster ID, gene by gene.
> > >
> > >     I know UCSC browser has the Affy array mapping info.
> > >
> > >     But I don't know which track or mySQL UCSC table is the current gold
> > > starndard for gene annotation.
> > >
> > >     Please advise.
> > >
> > >     Thanks
> > >
> > >     Guoliang
> > > _______________________________________________
> > > Genome maillist  -  Genome at soe.ucsc.edu
> > > http://www.soe.ucsc.edu/mailman/listinfo/genome
> > >
> >
>