Least Homology comparison

Charles A. Alexander charles at MEDINFO.ROCHESTER.EDU
Wed Jun 23 10:44:18 EST 1993


Hello

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 
for? 

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 
"Dis-Homology").

Oligo selection software does it on a per sequence basis.  Any suggestions?
My apologies if the question sounds more complex than it really is.

Thanks

Charles Alexander
University of Rochester Med. Ctr.
Div. of Medical Informatics,
601 Elmwood Ave., Box BPHYS
Rochester, New York 14642
FAXnet:		(716) 275-6007
AT&Tnet:	(716) 275-0643 									 																	

Internet:	Charles at Medinfo.rochester.edu
Bitnet:			GCGC at UORDBV




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