>Does anyone know of a program for designing oligonucleotides for
>use as hybridisation or PCR probes on the basis of protein allignment
>and codon usage?
There is a program in the GCG packages called BACKTRANSLATE (available at
darsebury) which does exactly that ie. you give it an amino acid sequence
(most homologous regions of you alignment) , a codon usage table (some are
already provided eg.Ecoli) and it will output either the most probable
sequence or the most ambiguous (excuse the spelling) depending on what
Its a great little program!
Hope this helps,
plxigpg at vax.ccc.nottingham.ac.uk