[Genome] Using MySQL Api To get a gene's sequence between a start and stop sight...

[Ann Zweig]

Hi Jay,

	If you are just looking for intergenic sequence between two genes, then the 
method you have described works fine.  Once you have the intergenic area 
displayed in the genome browser, you can also click on the "DNA" link in the top 
blue navigation bar.  This will give you the DNA sequence for the exact position 
you are viewing in the browser.

	For ease of navigation, try enabling the "Next/previous item navigation" on the 
configuration page (the 'configure' button from the genome browser).  Read more 
about this and other configuration options here: 
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning

	 It is not possible to extract the DNA using the MySQL public server, as the 
underlying sequence is not kept in a database table.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Jay Vyas wrote:
> Hi guys :  Im trying to figure out how run a query through the mysql
> interface that will return the entire intragenic region of 2 genes.  Can
> somebody post a sample query to do this ?
> 
> Currently the way I do this -
> 
>    Go to UCSC, enter the gene name (lets call it X).
>    Zoom in on the end of the gene preceding X (lets call this one Y)
>    Click on the end of the Y, write down the end nucleotide number (call
> this Yend)
>    Click on the beggining of X, write down this number (call it Xbeg)
>    enter in the value Yend-Xbeg in the position text field.
>    click on the image and uncheck all boxes other than 5' UTR
>    Download the sequence in fasta format.
> 
> --
> Thanks !!!
> Jay Vyas
> BioSystems Modelling Group/UCHC
> http://folding.uchc.edu
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