[Genome] Conserved UTR sequences

[Kayla Smith]

T Joshi,

It sounds like you have a good working knowledge of the Table Browser.

If you tack on the 100 base pairs to each item in your custom track, 
then you're going to be looking for an intersection between 
multiz28wayFrames and your new custom track.  You might not get exactly 
the same intersection results with the 100 base pairs region tacked onto 
each item, but you can play around with the X% overlap parameter in the 
intersection tool.

Another way to do this is to leave the your Table Browser configuration 
exactly as you say, except on the last step, when you have toggled 
"output" to "sequence" and you click "get output" you are taken to a set 
of Sequence Retrieval Region Options, and here you can add the 100 extra 
bases upstream (5').

A few things to note:

1.  It's not possible to choose both "multiz28wayFrames records that 
have at least 80% overlap with tb_ensGene" and "create basepair wise 
intersection" on the intersection page, which you have listed in your 
protocol below.  Chosing "any overlap" might be the best way to start out.

2.  You may want to use the multiz28way table rather than the 
multiz28wayFrames table.  The multiz28wayFrames table is used to create 
the codon translation (frame shift) display.

3.  Lastly, you could also make use of some pre generated upstream maf 
files in the download directory here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/maf/

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


T Joshi wrote:
> Hi !
> I create custom track on UCSC table browser to obtain conserved UTR
> sequences from teh table browser in following way:
> 
> - I select genes and gene prediction track from groups, and within
> that, ensembl genes to select ensGene table.
> - Output format as custom track
> - Pressing output button brings me to another page where i can select 5' exon
> - then i press the get custom track in table browser
> - Again I select comparative genomics group  and  Conservation track,
> - and table - multiz28wayframes
> - create intersection  with the ensGene table ( the custom track
> containing 5' exon)
> -  multiz28wayFrames records that have at least 80% overlap with tb_ensGene
> - create basepair wise intersection
> - submit
> - and then select "sequence" in the output format to obtain 5' UTR
> sequences which are conserved.
> 
> Now that I wish to find the promoter sequences for these genes. How
> can I obtain? Should I select exon + 100 bps to build the custom track
> of ensembl genes?
> 
> Is this a right approach?
> Awaiting for your valuable inputs.
> Thanks
> T Joshi
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