Commercial Mac Primer Design Software ?

BIOSCI plewniak at titus.u-strasbg.fr
Tue Dec 21 10:04:14 EST 1993


Hello world...

Jeff Martino asked :

>In your opinion what's the best _commercial_ Macintosh program for 
>PCR/sequencing primer design.

....

>Quote:  "I want to enter a template sequence, show the acceptable region of 
>the template I want the primer(s) to bind, and let the program choose the best 
>primer or pair -- minimized secondary structure, minimized self-dimer, 
>minimized dimer with other amplimer, etc."
>
>Any and all comments on your experiences are appreciated.
>
>--Jeff Martino



We use here Oligo which was written by Wojciech Rychlik (Rychlic et al. 1990,
Nucleic Acids Res. 18, 6409-6412) and is commercialised by :

		National Biosciences, Inc.
		3650 Annapolis Lane
		Plymouth, MN 55447
		USA

		Tel (800) 747-4362   /   (612) 550-2012
		Fax (800) 369-5118   /   (612) 550-9625

Distributor for Europe is :

		MedProbe
		Postboks 2640 St. Hanshaugen
		N-0131 Oslo 1, Norway

		Tel (47-2) 20 01 37
		Fax (47-2) 20 01 89

A PC compatible version is also available.

When we purchased it (Feb 92) the price was US$640 for non profit organizations
and US$800 for industry.


I don't know if this is actually the best one since it's the only one I've
ever used on a Macintosh (has anyone heard of another one?... ) but it 
certainly looks like one that might fit your requirements. You enter the
template sequence and specify the regions of acceptable primer annealing,
and you get a pair of oligos that fit the following requirements :

	- no significant self-dimer
	- no significant annealing between primers
	- overall oligo stability
	- 3'end stability
	- unique 3'ends
	- no homooligomers
	- no harpins

Results include : Tm for selected primers, amplification product, optimal
annealing temperature, extinction coefficient of products...


One interesting feature of Oligo is that it calculates Tm of short sequences
with the nearest-neighbour method described by Breslauer et al. (1986 PNAS 83,
3746-3750) for DNA and Freier et al. (1986 PNAS 83,9373-9377) for RNA.

Furthermore, if you're not satisfied with the standard method you may conduct
the search in a totally personalised way.

Finally, Oligo can be used for designing oligos for other purposes than PCR
(sequencing, mutagenesis, hybridisation).


Well, all this would be perfectly allright without some little problems...

First of all, Oligo does not actually search (automatically speaking...) for
the best pair of oligos but for the FIRST pair of oligos it could find that 
fit all requirements.

What's more, automatically selected primers cannot be of different size!!!



I can't think of anything else to say at the moment...

I hope this was of some help...


				Frederic PLEWNIAK
				LGME du CNRS
				11 rue Humann
				67085 Strasbourg Cedex - FRANCE
				Tel : (33) 88 37 12 55 #452
				plewniak at titus.u-strasbg.fr 






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