Oligo 4.0-s program

Tracy Aquilla aquilla at salus.med.uvm.edu
Thu Mar 16 10:42:08 EST 1995


In Article <D5CsDx.B9I at UQuebec.CA>, Pierre_Talbot at Infopuq.UQUEBEC.CA () wrote:
>We are in the market for a Macintosh PCR primer design program and thought: 
>OLIGO would be good, although the comments here make me think otherwise: what 
>about RightPrimer? And where do I get AMPLIFY?: 
>Pierre_Talbot at iaf.uquebec.ca: 
>X-Newsreader: TIN [version 1.2 PL2]
>

I have a few comments to add. OLIGO is an excellent program. One problem I
see is that it is fairly complex, because it has so many features. I think
many users do not take the time necessary to learn how to use the program
properly, and simply use the default settings. While this may work in some
cases, the default settings are certainly not optimal for most analyses.
When designing primers, I usually use OLIGO first to select my primers, then
I double-check my anticipated results using Amplify. While Amplify is a much
simpler program, it does a decent job of predicting whether a given set of
primers will work for PCR. This program also has variable parameters, and
the default settings seem to be pretty useful in most cases. One problem
with Amplify is that it will not automatically select a matched set of
primers for you, as OLIGO can. I don't think Amplify is a suitable
substitute for OLIGO. The capabilities of OLIGO are immensely greater than
those of Amplify. If you can afford it, I'd buy OLIGO and learn how to use
it. You can get Amplify from one of the molbio anon FTP servers. Try the one
at NCBI (ncbi.nlm.nih.gov) or IUBIO (ftp.bio.indiana.edu). Good luck.
    tracy



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