*Primer programs

Dan Jacobson DANJ at JHUHYG.bitnet
Sun Jan 19 18:46:58 EST 1992

A request was made for a program which will design PCR primers.
I have included the README file from the PRIMER program available via anonymous
ftp from genome.wi.edu.  Instructions for obtaining the program on disks are
included in the appended information.  PRIMER comes with a pretty extensive man
ual and is pretty user friendly.  I'll leave the rest to the following file.


Dan Jacobson
danj at jhuhyg.sph.jhu.edu


PRIMER 0.5:   Questions and Answers

What exactly is PRIMER?

PRIMER is a computer program for automatically selecting PCR primers.  PRIMER te

PRIMER was written by Steve Lincoln, Mark Daly, and Eric Lander at the MIT Cente

What types of computers does PRIMER run on?

In short: just about anything which supports a standard C language compiler, inc

(1) IBM PC and compatibles.  A PC/AT (286) class machine or better with 640K of

(2) Apple Macintosh computers.  A Mac II series or SE/30 with a math coprocessor

(3) Most Unix workstations including Sun SPARCStation and DEC DECStation systems

(4) DEC VAX/VMS computers under VMS Version 5 with VAX C.

How do I get PRIMER?

PRIMER is available from a number of sources:

(A) You can get PRIMER from another user, provided you strictly follow the terms

(B) You can download the most recent version off the Internet via anonymous FTP

(C) You can send a request to:

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

Email to "primer at genome.wi.edu" (Internet),  or  FAX to 617-258-6505

Request a copy of PRIMER, specifying a 3 1/2" floppy disk for either SPARCStatio

Do I really need to compile PRIMER myself, and if so, how?

If you receive a ready-to-run version from us or another user, then you do not.

The C source code we distribute may be compiled using:

(1) Microsoft C 4.0 on IBM PC compatibles.  The file MAKEPC.BAT included execute

(2) Apple Macintosh computers with ThinkC 4.0.1.  A ThinkC project file has been

(3) DEC VAX/VMS computers under VAX C with VMS 5.x.  The file MAKEVAX.COM includ

may have to change the linking procedure depending on your system's configuratio

(4) Unix workstations including Sun SPARCStation and DEC DECStation Systems with

Before compiling the program, you may need to modify configuration information i

What's the fine print?

PRIMER and its documentation are copyright 1991 by the Whitehead Institute for B

PRIMER is available for free use for non-commercial purposes by basic research l

PRIMER may be freely redistributed to other scientists, provided that all of the

Primer is designed to select primers for PCR applications, although it may may a

PRIMER is supplied without any warranty or guaranteed support whatsoever.  The W


They are:

File              Description
----              -----------
primer.c          PRIMER C Source Code
text.c            PRIMER C Source Code
primer.h          PRIMER C Source Code
sample.seq        Sample Input Sequence File
sample2.seq       Longer Sample Input Sequence File
standard.cri      Sample PCR Primer Criteria File
sample.rep        Sample Repeat Sequence File (Human Alu only)
mouse.rep         Sample Repeat Sequence File (Mouse Sequences)
rat.rep           Sample Repeat Sequence File (Rat Sequences)
human.rep         Sample Repeat Sequence File (Human Sequences)
manual.txt        PRIMER Manual text file (no line breaks)
manual.asc        PRIMER Manual text file (with line breaks)
readme.txt        This Document (text file, no line breaks)
readme.asc        This Document (text file, with line breaks)
makepc.bat        DOS Batch file to compile PRIMER
makevax.com       VAX/VMS Command file to compile PRIMER
makefile          Unix Makefile to compile PRIMER

Other files which may be included with specific versions include:

File              Description
----              -----------
primer            PRIMER Executable for Sun SPARCStations
primer.exe        PRIMER Executable for PC Compatibles
PRIMER            PRIMER Executable for Macintosh
PRIMER Manual     PRIMER Manual (Mac Microsoft Word 4.0 Format)
The PRIMER Manual PRIMER Manual (Macintosh Executable)
PRIMER README     This Document (Mac Microsoft Word 4.0 Format)
The PRIMER README This Document (Macintosh Executable)

Remember, to legally redistribute PRIMER to anyone else, you must give them unmo

Steve Lincoln and Mark Daly
MIT Center for Genome Research
Whitehead Institute for Biomedical Research
9 Cambridge Center, Cambridge, MA  02142
primer at genome.wi.edu,  FAX:  617-258-6505

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