IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Wanted:Oligo/Primer Shareware

Francis Ouellette francis at monod.Biol.McGill.CA
Tue Feb 2 23:35:25 EST 1993


caminak at ubvmsb.cc.buffalo.edu (Ichiro Nakamura) writes:

>To anyone:   Our lab is looking for a program (Shareware if available)
>to find primers/oligos.  We have looked at Hitachi's OLIGO program, but
>it is expensive and much more comprehensive than we need at this time.
>Any information would be appreciated.  


from the methods_and_reagents FAQ (Frequently Asked Questions):



*******************************************************************
*                                                                 *
*                Frequently Asked Question (FAQ) list             *
*                for bionet.molbio.methds-reagnts                 *
*                                                                 *
*                Last update was on 29 January 1993               *
*                                                                 *
*******************************************************************

My intention for creating this FAQ list is not to attempt a
comprehensive review of the subjects discussed within the
newsgroup bionet.molbio.methds-reagnts, but rather to provide
a quick resource for first time users. Many of the questions
answered below are asked by people new to the group on a recurring
basis.

This FAQ list is available by anonymous ftp to ncifcrf.gov
Simply get the file pub/methods/FAQlist

If anyone would like to make additions or corrections to
the FAQ list, please send the information to:

Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Frederick, Maryland 21702-1201 USA

e-mail: pnh at ncifcrf.gov 

================================================================================
12. What kinds of programs are available for designing PCR primers?


What kinds of programs are available for designing PCR primers?

There are four programs which deal with pcr primer construction which one
can obtain by anonymous ftp and one which will be mailed to you by the author.
The programs are:

1. Pgen - for DOS only

PrimerGen searches strings of amino acid residues in order to reverse-translate
oligonucletide primers of a desired range of lengths and maximum number of
degeneracies.

PrimerGen only works on IBM-PC(TM), XT, AT, PS/2 and compatibles with
EGA or VGA graphics adaptors.  It will not work on computers with CGA or
Hercules(TM) graphics cards. A hard drive is NOT required and PrimerGen will
fit on a 360K 5.25" floppy disk.

PrimerGen contains a sequence editor where amino acid residues are entered.
The amino acid sequence must be ONE fragment and cannot be longer than 70
residues.  The sequence must be in the ONE LETTER CODE and cannot contain
any UNKNOWNS.  After the desired amino acid sequence has been entered have the
option of saving the sequence to a disk. PrimerGen will also accept and
re-edit previously saved sequence files, and also contains a codon preference
table editor. You can get this program by anonymous ftp at
ftp.bio.indiana.edu. It is found in the molbio/ibmpc directory.

2. Primer - Stanford - Sun Sparcstations only 

The program 'primer' is written by Don Faulkner. It helps to find potential
mispriming sites (primer sequences should be designed before running the
program!). The program gives higher weights to matches at the 3'
end of the primer, linearly decreasing them towards the 5' end (the default
is weight=10 for 3' nucleotide decreasing to 1 at nucleotide # 8 from the 3'
end). The program can be used when amplifying *long* fragments from a known
sequence. The program is written in "C" and runs on Sun workstation (Unix).
You can get the program by anonymous ftp at 36.45.0.126 or contact
James Mullins jmullins.stanford.edu (415) 723-0668.

3. Primer - Whitehead -Unix, Vms (and DOS and Mac if you can compile it)

PRIMER is a computer program for automatically selecting PCR primers
written by Steve Lincoln, Mark Daly, and Eric Lander.

PRIMER will run on just about anything which supports a standard C
language compiler.
- IBM PC and compatibles.  A PC/AT (286) class machine or better with 640K of
- Apple Macintosh computers.  A Mac II series or SE/30 with a math coprocessor
- Most Unix workstations including Sun SPARCStation and DEC DECStation systems
- DEC VAX/VMS computers under VMS Version 5 with VAX C.

PRIMER is available from a number of sources:
- You can get PRIMER from another user, provided you strictly follow the terms
- You can download the most recent version off the Internet via anonymous FTP
- You can send a request to:

          PRIMER c/o The Lander Lab,
          Whitehead Institute/MIT
          9 Cambridge Center, Cambridge, MA 02142.

E-mail to "primer at genome.wi.edu" (Internet), or FAX to 617-258-6505
You can also get PRIMER by anonymous ftp from genome.wi.edu in the
distribution/primer.0.4 directory.

4. Amplify - MAC only

This 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.

You can obtain a copy of Amplify from 
sumex-aim.stanford.edu via anonymous ftp. Look for the file:

      /info-mac/app/amplify-10.hqx

The author, Bill Engels, can be reached at WREngels at wisc.macc.edu


5. OSP - Unix, X-windows, Vms, DOS, Mac - by snail-mail only.

OSP is available for free, but the university lawyers require that you
sign a licensing agreement. The legal document is not for the
paperwork faint-at-heart. It is quite long and daunting. If you're
waiting for the legal stuff before starting your experiment, you
may be better off working out a primer by hand.

Here is the abstract from the 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 at 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.


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



regards to all,

francis


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I & XVI sequencing project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis at monod.biol.mcgill.ca




More information about the Bio-soft mailing list

Send comments to us at archive@iubioarchive.bio.net