Looking for a good oligo design program. Help!

Basavaraju Shankarappa bsh at MED.PITT.EDU
Mon Sep 28 08:59:33 EST 1992


Here is some program that may be quite useful.  We have been using
OLIGO to look at our primers.  Everytime we use it, the inventor of tat
program goes to higher hell because of our curses.  I think it is one
program that people did not want anybody to make use of.  The manual is
so unfreindly you just donot feel like using it.

The PRIMER program looks like a very good program at least from their
descriptions.  The logic and methodology has been explained quite
decently and all of it does make sense.  Specially they have used 
a base stacking method to calculate Tm of the primers and it is supposed
to give a single value for the Tm which is much less pain (however accurate)
than the 3 outrageously different Tm provided by OLIGO.
	I have not been able to use the program yet because I have not been
able to compile the program with my knowledge and available facilities.
I believe they will supply a executable program if requested.  So I am
waiting.  If anyone else has had the opportunity to use it by now, I would
appreciate their input.  

	You can download the source codes and all the files by ftp as below.
You have to acknowledge the receipt of the program for some proprietory
considerations.  
To get the primer program

by anonymous.ftp

ftp 
to 

genome.wi.edu
and copy the programs from the folder

distribution/primer.0.4


or Contact Dr. Eric Lander 
Whitehead Institute for Biomedical Research
9 Cambridge center
Cambridge  MA 02142


Hope to see some discussion.
Raj Shankarappa
Univ of Pittsburgh



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