[Genome] Custom Annotations locally

[Brooke Rhead]

Hi Vinayak,

I think I understand your question better now.  We don't actually have 
any XMs annotated in the Genome Browser.  One of our developers suggests 
using the N-SCAN or AUGUSTUS tracks (AUGUSTUS is only available on hg17) 
for high-quality gene predictions.  With those you can use the procedure 
I described.

If you specifically want the XMs, however, you can BLAT them (as you 
suggested in your original question).  You can then turn your BLAT 
results into a custom track in order to view the transcription starts 
and ends and fetch sequence.  To do this, set the BLAT output type to 
'psl no header', then copy and paste the row(s) of interest into the 
custom track input.  (Hit the 'add custom tracks' button.  PSL is one of 
the accepted file formats.)  If you do this with the mRNA sequence, you 
will see the transcribed region of the gene prediction.  You will need 
to repeat the process with the protein sequence to see the translated 
region of the gene prediction.

Once you have custom tracks of translated and transcribed regions, you 
can use the intersection tool in the Table Browser to get the 5' and 3' 
UTRs.  You can choose to output the results of the intersection as a 
third custom track, or just output the sequence directly from the 
intersection.

I hope this solution works for you.  Let us know if you need 
clarification on any of the above steps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Vinayak Kulkarni wrote:
> Thank you for your email. How do I get annotations for predicted genes 
> (XM's)? You have all the validated genes there. Is there a way to get 
> the predicted genes too?
> Thanks again,
> Kind regards,
> Vinayak.
> 
> On 6/7/07, *Brooke Rhead* <rhead at soe.ucsc.edu 
> <mailto:rhead at soe.ucsc.edu>> wrote:
> 
>     Hello Vinayak,
> 
>     The Table Browser will allow you to extract sequence for 5' UTRs and 3'
>     UTRs in our gene prediction tracks.  Just choose that particular track
>     in the the Table Browser (the "tables" link at the top of the page),
>     enter the position of interest or some gene identifiers, and choose
>     "output format: sequence".  If you choose to output the genomic
>     sequence, you will see options for selecting the 5' or 3' UTRs, and for
>     adding bases upstream and downstream of the selected gene regions.
> 
>     More detailed information is available in our Table Browser User's
>     Guide:
> 
>     http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
> 
>     Specifically, see the instruction on displaying sequence data:
> 
>     http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence
>     <http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence>
> 
>     I hope this answers your question.  If not, please feel free to write
>     back to this list.
> 
>     --
>     Brooke Rhead
>     UCSC Genome Bioinformatics Group
> 
> 
> 
>     Vinayak Kulkarni wrote:
>      > Hi,
>      > I wanted to provide each gene annotations such as it's 5' UTR, 3'
>     UTR, be
>      > able to pull out information upstream/downstream say Xkb as per the
>      > requirement. I know you guys have all this data on your browser
>     tables but I
>      > cannot find data annotated for predicted genes.
>      > So essentially want I want is a way to annotate for a given gene
>     (including
>      > predicted genes), the genomic region (BLAT like o/p) with introns
>     and exons
>      > and be able to extract the 5' & 3' UTR along with given length of
>     upstream
>      > or downstream sequences. Can you please advice?
>      > Thank you in advance,
>      > Kind regards,
>      > Vinayak.
>      >
>      >
> 
> 
> 
> 
> -- 
> --
> "Hesitating to act because the whole vision might  not be achieved, or 
> because others do not yet share it, is an attitude that  only hinders
> progress"... Mahatma Gandhi