Primers for RTPCR

Keith James bss194 at pwilliams.bangor.ac.uk
Fri Oct 9 05:33:36 EST 1998


>>>>> "David" == D C Wilcockson <bsp04d at bangor.ac.uk> writes:

    David> Simply, I need to design specific primers to cDNA from a
    David> crustacean neurohormone. All I have to go on is the amino
    David> acid sequence and decapod crustacean codon usage tables
    David> which I have gleened from other's work.

If you have the codon usage table and some peptide sequence then the
GCG program BACKTRANSLATE will give you a table of possible
backtranslations and the most and/or least ambiguous sequences. It
also gives a running score of the probability that the next 4 codons
will all be the most common for their respective aa.

You can then use this to guide your choice of primers. You may be able
to take the sequence into your PCR primer design software if it
respects IUB codes.

-- 
Keith James  --  k.james at bangor.ac.uk  --  http://www.bangor.ac.uk/~bss194 
Biodegradation Group - School of Biological Sciences - University of Wales
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