From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson)
Newsgroups: bionet.software
Subject: OSP - another primer program
Date: 14 Apr 92 16:18:52 GMT
Article-I.D.: welchgat.9204141618.AA24333
Distribution: bionet


Hmm, I sent this yesterday and it bounced - see if this goes through.
Now of course we need to add John Nash's program to the list.

                          ----------------

During this recent rehash of the discussion about primer designing
programs I remembered another program which is available to the
community although not by ftp.  I dropped Phil Green a note about this
program and (with his permission) am including his response.

Best of Luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu

==============================================================================


Dan,

  OSP (which was developed by LaDeana Hillier and me -- LaDeana
deserves most of the credit) is available for free, but the university
lawyers here require that you sign a licensing agreement (primarily to
protect us from Perkin-Elemer/Cetus and malpractice lawsuits) and for
that reason don't want us to make it available by ftp.

Here is the abstract from our paper describing OSP, which appeared in
PCR Methods and Applications 1, 124-128 (1991), along with information
on how to get the program.

ABSTRACT

OSP  (Oligonucleotide Selection Program)
selects oligonucleotide primers for DNA sequencing and the
polymerase chain reaction (PCR).  The user can specify (or
use default) constraints for primer and amplified product lengths,
%(G+C), (absolute or relative) melting temperatures, and
primer 3' nucleotides.  To help minimize non-specific priming and
primer secondary structure, OSP screens candidate primer sequences,
using user-specifiable cutoffs, against potential base pairing with a
variety of sequences present in the reaction, including the primer
itself, the other primer (for PCR), the amplified product, and any
other sequences desired (e.g., repetitive element sequences in genomic
templates, vector sequence in cloned templates, or other primer pair
sequences in multiplexed PCR reactions).  Base pairing involving the
primer 3' end is considered separately from base pairing involving
internal sequences.  Primers meeting all constraints are ranked by a
``combined score'', a user-definable weighted sum of any of the above
parameters.

OSP is being routinely and extensively used to select sequencing
primers for the  C. elegans genome sequencing project, and human
genomic PCR primer pairs for the Washington University Genome Center
mapping project, with success rates exceeding 96% and 81%
respectively. It is available for research purposes from the authors,
at no cost, in both text output and interactive graphics (X windows)
versions.

AVAILABILITY

C language source code for OSP is available (for research purposes only)
at no cost from the authors,  in either the text
output version (tested for VAX/VMS, PC, MAC, and SUN Sparcstations),
or interactive X windows graphics version (tested for SUN Sparcstations).

 To obtain OSP please send your postal address either to Phil Green by email,
(pg@genome.wustl.edu) or (preferably) by FAX to (314) 362-2985 c/o Paula,
the secretary handling OSP requests.  You must provide a signed licensing
agreement (which she will send you) and a stamped addressed mailer with
diskette before the program can be sent to you. Sorry for the formalities.

Phil Green