Sequence searches

Patrick Phillips patrick at wbar.uta.edu
Wed Sep 21 15:15:15 EST 1994


I'm interested in searching the C. elegans database for specific short
DNA sequences (I'm looking for RAPD priming sites).  The DNA analysis
window with the Genome_Seq keyset provides the ideal method, except that
one is limited to only three 10-mers because of the finite length of
text input bar.  This seems like a serious user interface limitation
(i.e., the text bar does not scroll, but just stops at about 40
characters).  I would like to do many searches simultaneously, so this
is a problem.

I've tried to figure out the Query equivalent to the DNA analysis window,
but I'm afraid that even after three years of dabbling with it, I still
don't fully understand how the query syntax works.  Trying something
simple like

   find Sequence DNA=*tgcggctgag*

doesn't find anything, so I must be barking up the wrong tree.

It obviously must be possible to do this, so could someone out there tell
me what I'm doing wrong?

It is truly amazing to be able to do searches like this on over 6 Megabases
on my own computer.  I thank everyone who has contributed to this tremendous
resource.

Patrick Phillips
Biology Department
University of Texas at Arlington
patrick at wbar.uta.edu
(817) 273-2409





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