Path: utzoo!utgpu!watserv1!watmath!uunet!snorkelwacker!bionet!nfl.afrc.ac.uk!PAU
From: PAU@nfl.afrc.ac.uk
Newsgroups: bionet.software
Subject: Designing oligonucleotide probes from protin alignments
Message-ID: <9009121717.AA05102@genbank.bio.net>
Date: 12 Sep 90 17:38:00 GMT
Sender: daemon@genbank.bio.net
Lines: 9

I need a program to assist in designing oligonucleotides for hybridisation
probes and PCR primers.  The problem is basically this: given a protein
alignment (or section thereof) and a codon usage table, what is the most
probable DNA sequence of an as yet unidentified gene encoding a protein of the
same class. This has to include the probability of the likeliest base at
each position, enabling one to slide a window of given width down the
probability profile to identify maxima, which can then be used to synthesise
probes.  Any offers?
Martin Drummond, Nitrogen Fixation Lab, Sussex.