Primer design freeware for Mac?

Paul St. Amand PST at KSU.KSU.Edu
Tue Dec 20 10:46:12 EST 1994


In article <3d220p$1e4 at nntp1.u.washington.edu>, cdarby at u.washington.edu
(Creg Darby) wrote:

PSt> Is there free software available for Macintosh for designing PCR primers? 
PSt> If so, where can I find it, and how user-friendly, versatile and reliable 
PSt> is it?
PSt> Thanks, and apologies if this has been covered here before.

Here are four (Amplify, OSP, Primer, and Primers), there may be others
also. All have their strengths. Just try them out, you'll find them very
useful. Info on each below. I think Amplify, Primer, and Primers can be
found at ftp.bio.indiana.edu in the /molbio/mac directory. OSP is free,
but must be had from the author, see below.


*******************************************************************************
PRIMER: A Computer Program for Automatically Selecting PCR Primers
Version 0.5, May 1991

by Stephen E. Lincoln, Mark J. Daly, and Eric S. Lander
MIT Center for Genome Research and
Whitehead Institute for Biomedical Research
Nine Cambridge Center
Cambridge, Massachusetts 02142

Send Inquiries to "Primer c/o The Lander Lab" at the above address.
Email to "primer at genome.wi.edu" (Internet) or "lander at mitwibr" (Bitnet)
FAX 617-258-6505

PRIMER is copyright 1991 by The Whitehead Institute for Biomedical
Research, all rights are reserved.  PRIMER may be freely used and
distributed, but only under specific conditions as outlined in the license
included in this document.  Any other use is a violation of applicable
laws and regulations.

(1) INTRODUCTION

PRIMER is a computer program for selecting PCR primer pairs to amplify
specific regions of sequenced DNA.  While PRIMER was specifically designed
to select primers from cloned and sequenced genomic DNAs, many of the
tests it performs are useful for selecting oligos for other types of
experiments as well, including other PCR applications, oligo hybridization
and dideoxy sequencing.

For any given sequence, PRIMER applies a variety of analyses which determine:

(1) which "target" subsequence should be amplified 

(2) which of the possible primers flanking the target will be compatible
with specific PCR reaction conditions, such as annealing temperature. 
(PRIMER computes annealing temperature based on recent experimental
measurements of base-stacking energies, rather than simply counting A-T
and G-C basepairs.  We find that it improved our success rate.)

(3) whether the primers (or the target sequence itself) have a significant
degree of complementarity to known repeat elements (such as Alu), possibly
resulting in nonspecific annealing and amplification.

(4) whether the primers have a significant degree of complementarity to
themselves or to each other.

(5) whether the PCR product itself has the desired size and GC content.

Once configured for specific criteria, PRIMER can apply these tests to
many input sequences in an automated manner.  PRIMER also allows you to
interactively test specific primers you have selected by hand (with or
without the computer's advice) against these criteria.
*******************************************************************************

OSP: OLIGO SELECTION PROGRAM, User Documentation
Program Author: LaDeana Hillier

INTRODUCTION
   OSP is a computer program developed to aid in selecting
oligonucleotide primers for DNA sequencing and for the polymerase
chain reaction.  OSP allows the user to specify (or use default) 
constraints for primer and amplified product lengths, %G+C contents,
and (absolute or relative) melting temperatures; for primer 3' 
nnucleotides; and for the maximum allowable primer-self,
primer-primer, and primer-product annealing propensities.
Candidate primer sequences are screened against a user-supplied
data set of other sequences (e.g. repetitive element or vector
sequences) to help minimize the possibility of non-specific priming.
Primers meeting all constraints are ranked and displayed in order of 
increasing overall ``score'', which is a user-definable weighted sum 
of the above parameter values.

   OSP is currently being routinely used both for sequencing primer
selection in the St. Louis/Cambridge nematode sequencing project and to 
generate PCR primers for the YAC/STS mapping project in the St. Louis 
Human Genome Center, with a high success rate in both projects.
In comparison to other primer selection programs we have examined, OSP
is unusual in the range of user settable parameters employed (for example,
annealing propensity involving of the internal primer sequence can be scored
differently from annealing propensity at the 3' end), in allowing
pre-screening against other sequences, and in the
flexibility allowed the user in setting constraints and ranking candidate
primers.  This flexibility allows the user's selection criteria to
evolve in the light of laboratory experience.

   The program is available at no cost from the authors in two
versions, one of which produces text-only output, and the other
having an interactive X windows graphic interface.
The interactive X windows version of the program also provides the
capability to call up trace and sequence data (using the ted trace editor)
from both the ABI 373A or Pharmacia ALF fluorescent sequencing machines.

PROGRAM DISTRIBUTION AND INFORMATION

Additional information can be found in the following:
   Hillier, L. and Green, P. (1991) 
 OSP: A computer program for choosing PCR
 and DNA sequencing primers. PCR Methods and Applications 1:124-128.

Please direct all comments and suggestions to the author, LaDeana Hillier:
email: lfw at elegans.wustl.edu
Phone: 314-362-7667
regular mail:  Washington University Medical School
               Department of Genetics
               Box 8232
               4566 Scott
               St. Louis, MO  63110 USA
*******************************************************************************


PRIMERS

This is a Macintosh program for designing primers for PCR.  Sequences can be
entered by hand, from plain text files, from DNA Inspector files, or from
IBI MacVector files.  Up to 10 forward and 10 reverse primers can be
compared.  The program uses the method of Rychlik and Rhoads to calculate
the thermodynamics of melting.  Possible interfering secondary structures
between primers and target are also shown.

Instructions for use are given in the HELP section of the About Primers...
menu item under the Apple Menu.

The program is a SuperCard standalone project.  It uses 1600K of memory,
which is characteristic of these projects.  The color looks reasonably
good if your monitor is set to 256 colors.  System 7 compatible.

This is freeware.  We make no claims for the efficacy of PRIMERS for any
commercial or educational use.  You may freely copy PRIMERS, but do not
change the authorship or credits.

Version 1.2 of Primers for Macintosh.

Any bugs or problems, please email Greg Bristol at
the Lab of Molecular Medicine and Structural Biology
(formerly LBES):  gregb at lbes.medsch.ucla.edu
*******************************************************************************

AMPLIFY 1.2

    This Macintosh software is for use in designing, analyzing, and
simulating experiments involving the polymerase chain reaction (PCR). PCR
is a technique used by molecular biologists to amplify highly selected
segments of DNA. If you never heard of PCR, you probably have no use for
this program. 

    To use Amplify you must supply the sequences of the primers and the
target DNA. The software then analyzes the combination of primers and
target sequence you have chosen to determine what portions of the target
are likely to be amplified. The result is a graphical map of the target
sequence, primer binding sites and amplified fragments. The program also
provides various bits of helpful information about the reaction products,
primer binding sites, potential dimer formation, etc., that can help in
planning a PCR experiment and designing primers.

     Version 1.2 fixes a few bugs. There are no new features since version 1.0.

Send questions and comments to me at the addresses below, preferably by e-mail.
-----------------------------------------------------------------------------
Bill Engels                           :                WREngels at macc.wisc.edu
Genetics Department                   :                office: (608) 263-2213
University of Wisconsin               :                   lab: (608) 262-5578
Madison, WI  53706                    :                   FAX: (608) 262-2976
-----------------------------------------------------------------------------
*******************************************************************************

Paul C. St. Amand    (PST at KSU.KSU.Edu)
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