Here's an interesting problem. One of the researchers here needs to detect
expression of specific sequences in an experiment. But, the twist is this.
He works with a group of sequences. He wants to design probes unique to each
one of these sequences. The probe regions have to be fairly large (200-500bp).
Question is how do you determine which region in the sequence to make the probe
Also, GCG's PILEUP run with default parameters indicates about 75% homology in
the 3 sequences. The PRETTY program using the .MSF file as input was then run
with first the /DIFF qualifier and again with the /CASE qualifier.
Neither, result shows much promise. I also attempted a PROFILEMAKE and later
realized that it would work if you were looking only for homology (not
Oligo selection software does it on a per sequence basis. Any suggestions?
My apologies if the question sounds more complex than it really is.
University of Rochester Med. Ctr.
Div. of Medical Informatics,
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