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.