comparison of GC content

john peloquin peloquin at galaxy.ucr.edu
Mon Jun 29 13:31:12 EST 1998


Dear Netters,

We wish to probe genomic southern blots with probes derived from two different genes.
One gene is a transposable element, and the other is a very large transmembrane
receptor molecule.

We wish to use probes that are comparable in their GC content. Essentially, we want to take
a portion of the transposable element and make a probe with it. We also wish to subsequently 
probe the same southern with a probe derived from the transmembrane molecular genomic clone that
has a similar GC content- we want to compare the relative (and absolute) frequency of these
sequences in the target animal genome through the relative intensity of probe autoradiography.
The similar GC content would minimize the possible contribution of different GC content in the 
amount of probe hybridizing after washes.

I thought of using some of the GCG programs like GAP or BESTFIT, but of course, they would 
only show sequence similarity- which if close enough would introduce another set of problems.
Ideally, we would like to use a 500 bp or so region of the receptor genomic clone that was close
as possible to the similar size probe derived from the transposable element.

Any suggestions would be most appreciated.


-- 
"Never Ascribe to Malice that which can be explained by Ignorance."
John J. Peloquin
Entomology, University of California, Riverside, CA 92521



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