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

[Jay Vyas]

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.

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Thanks !!!
Jay Vyas
BioSystems Modelling Group/UCHC
http://folding.uchc.edu