*Primer programs

Dan Jacobson danj at WELCHGATE.WELCH.JHU.EDU
Fri Apr 10 17:13:17 EST 1992

Patrick Twomey writes:

>>I'm looking for a primer analysis software (commercial or share-)
>>for Mac Intosh;
>>What could be the best choice
>>The purpose is to analyse multiple proteines sequences and get the best
>>pair of primers for PCR
>>Thaks a lot for spending time on this
>>jreich at illite.u-strasbg.fr
>>Regards, Jean-Marc
>We just bought Oligo 4.0 from National Biosciences(3650 Annapolis Lane,
>Plymouth, MN 55447 USA, (800)747-4362.)  We haven't had a chance to use it
>much, but it looks impressive, though it is a bit pricey: $800, $640 to
>non-profit orgs through 9/30/92.  From their propaganda:
>"Oligo will design and select your PCR primers, sequencing primers and
>hybridization probes, calculate primer annealing temps, molecular weights,
>ug/O.D., pM/O.D., and other useful data.  Oligo, using highly accurate nearest
>neighbor thermodynamic algorithms, automatically searches for and selects
>optimal PCR primers which are highly specific, free of homooligomer, dimer and
>hairpin structure, unique and fall within a user-specified Tm range.

Hmm, something is missing here.  The original request was for a program
which looks at multiple PROTEIN sequences and chooses pcr primers.
I assume that Jean_Marc is looking to pull up new members of a Superfamily,
say protein kinases, and has an alignment and wants to choose the best
pcr primers from that.  Now the propaganda from Oligo doesn't say anything
about looking at protein sequences for primer designation - if it actually
does this - great!, if not there are at least two programs (one of which I know
has been compiled on a Mac) which design primers which are FTP`able. 
Off-hand I can't think of an FTP`able program which looks at protein
sequence and designs primers.  
I still have the info from a a few months ago where there was a rather
lengthy thread on the ftp`able primer programs and will pass it along to
anyone who is interested.  As usual I'll repost it if the demand becomes large.

Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu

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