Designing oligonucleotide probes from protin alignments

PAU at nfl.afrc.ac.uk PAU at nfl.afrc.ac.uk
Wed Sep 12 12:38:00 EST 1990


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.




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