PCR primers design

Benny Shomer bshomer at ebi.ac.uk
Thu Jan 11 07:38:15 EST 1996

Hsien-wei Peng (hwpeng at ibms.sinica.edu.tw) wrote:
: Dear Netters,

:   I am searching for a software for PCR primers design which works on windows 
: (3.1 or 95) or DOS.  I would like a free one, but information about other 
: commercial products are also welcome.  Thank for your answering in advance.

On the EBI ftp server (ftp.ebi.ac.uk) you may find in /pub/software/dos
the following:

File: mismatch.txt. 
     Update: 15-Apr-1992. 
     Version: ?. 
     Size: 12 k 
     Compressed: -. 
     Author: Davidow L. S. 
     Description: Selection of PCR designed mismatch primers 
     Literature: CABIOS 8 (1992), 193 
     Source Code: Basic 
     SW Requirements: Basic interpreter/compiler 
     HW Requirements: - 

File: pgen11.exe. 
     Update: 14-Apr-1992. 
     Version: 1.1. 
     Size: 45 k 
     Compressed: PAK. 
     Author: Nash J. H. E. 
     Description: Oligonucleotide primer design by reverse-translation of amino acid sequences 
     Literature: CABIOS 9 (1993), 469-471 
     Source Code: - 
     SW Requirements: - 
     HW Requirements: VGA or EGA graphics card required 

Also, information obtained from the BioCatalog maintained at EBI 

AC             BC00429
NAME           Primer Design
DOMAIN         Oligomer design and synthesis
DESCRIPTION    PrimerDesign is a DOS-program to choose primer for PCR or
DESCRIPTION    oligonucleotide probes. It is tailored to check known 
DESCRIPTION    sequences for repeats and unique sequences and subsequencly
DESCRIPTION    to create prober primers according to this data. A lot of 
DESCRIPTION    constrains are available to meet your conditions. It can
DESCRIPTION    handle up to 31500 base pairs.
DESCRIPTION    Additional features: Unique sequences, repeats, restriction sites
AUTHOR         Andreas Becker, Joerg Napiwotzki
RA             Napiwotzki J., Becker A., Damian M.;
RT             "Primer Design - a new program to choose PCR primers
RT             and oligonucleotide probes.";
RL             Medizinische Genetik, Programme and Abstracts, Vol. 2 (1995).
AB             This paper is available
ADDRESS        Andreas Becker
ADDRESS        Friedrich-Ebert-Strasse 36
ADDRESS        35039 Marburg, Germany
CONTACT        becker at ps1515.chemie.uni-marburg.de
SITE           ftp anonymous ftp.chemie.uni-marburg.de
SITE           Directory /pub/PrimerDesign
SITE-CONTACT   becker at ps1515.chemie.uni-marburg.de
SITE           WWW Server at URL http://www.chemie.uni-marburg.de/~becker/pdhome.html
OS             PC (DOS)
LANGUAGE       Basic
VOLUME         -
REQUIRES       -

(Inspite of what is documented here, as far as I can recall, primer-mit is
also available for PC's. It worths asking them, since this is an excellent

AC             BC00158
NAME           PRIMER - MIT
DOMAIN         Oligomer design and synthesis
DESCRIPTION    PRIMER is a computer program for selecting PCR primer pairs to
DESCRIPTION    amplify specific regions of sequenced DNA.  While PRIMER was
DESCRIPTION    specifically designed to select primers from cloned and
DESCRIPTION    sequenced genomic DNAs, many of the tests it performs are useful
DESCRIPTION    for selecting oligos for other types of experiments as well,
DESCRIPTION    including other PCR applications, oligo hybridization and
DESCRIPTION    dideoxy sequencing.
AUTHOR         Lincoln S., Daly M. and Lander E.
RT             -
ADDRESS        MIT Center for Genome Research
ADDRESS        Whitehead Institute for Biomedical Research
ADDRESS        Nine Cambridge Center, Cambridge, Massachusetts 02142,USA
CONTACT        primer at genome.wi.edu
SITE           ftp anonymous genome.wi.edu
SITE           Directory /pub/primer.0.5
OS             Unix workstations including Sun SPARCStation 
OS             and DEC DECStation systems
LANGUAGE       C  
VOLUME         -
COMMENTS       PRIMER is available for free use for non-
COMMENTS       commercial purposes by basic research labs in 
COMMENTS       both academia and industry, providing users 
COMMENTS       register using the form supplied with the 
COMMENTS       program.

I hope this helps,

Doing PCR?
Have you got some good, working primers???
Visit the PCR primers database at http://www.ebi.ac.uk/primers_home.html
and make your donation.

If you don't have access to WWW, just write to primers at ebi.ac.uk

Benny Shomer
External Biological Liaison Officer,
EMBL outstation - The EBI,
Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK

Tel:   +44-223-494437
Fax:   +44-223-494468
Email: bshomer at EBI.ac.uk


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