PCR software

Bruce Roe broe at aardvark.ucs.uoknor.edu
Sun Jun 13 07:57:00 EST 1993

In article <1993Jun13.111453.3405 at aristo.tau.ac.il>, pc386 at ccsg.tau.ac.il (BENNY SHOMER 9238) writes...
>I am using Amplify for the MAC, only following a thorough analysis with the
>'Primer' software. The later is installed on the Weizmann Inst. Unix server
>dapsas1, but is avail. as a source or as a compiled version for PC (don't
>know if a MAC version is avail.). I don't have the exact data regarding the
>location of sources, but these can be looked up at the bionet archives.

	From the Primer's readme.asc file:


PRIMER is available from a number of sources:

(A) You can get PRIMER from another user, provided you strictly
follow the terms listed below and included with the program.  We
expect PRIMER to be mostly distributed this way.

(B) You can download the most recent version off the Internet via
anonymous FTP to "genome.wi.mit.edu" (internet number
Fetch and read the file README for details.  If this all sounds
like gibberish, please ask a computer specialist for help - the
process of receiving free programs off the network is actually
yMquite straightforward and commonplace to those familiar with
network access and some programming.  Currently, the C source code is
available (by ftp) which you may then compile on any machine using your
C compiler.  In addition, a DOS executable, primer.exe, and a MAC
executable (BinHexed), primer.hqx, are also available.  If you take one
of these executables, you should still download the entire contents of
this directory as it contains many additional files which PRIMER uses.
To transfer the DOS executable program, you must use the BINARY mode
in FTP.  The other programs and files should be fetched in
the TEXT mode.  This is the fastest way to obtain PRIMER.

(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.mit.edu" (Internet),  or  FAX to 617-258-

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>'Primer' is an excellent software that takes a target sequence, produces all
>possible primers from it, and then checks each potential primer against
>predefined criteria. The end result is a couple of the most optimal primers
>match, and two files, containing forward or reverse potential primers. These 
>can be checked manually by 'primer' on a second round. It also predicts the
>Tm of the primers quite accurately.
>Although I do all these analyses, as well as later on - running my potential
>primers through a FASTA session, to avoid 'lighting up' of unwanted targets,
>I do get into situations that primers don't perform under any circumstances,
>and I have to make new ones.
>Hope this helps. Benny.
> **************************************************************
>* Benny Shomer                                                 *
>* Tel-Aviv University                                          *
>* Sackler School of Medicine, Dept.of Embryology and Teratology*
>* Snail:  Ramat-Aviv , Tel-Aviv  69978 ,  Israel.              *
>* E-mail :  pc386 at ccsg.tau.ac.il                               *
>* Tel :  972-3-640-9238     FAX :   972-3-642-2046             *
>*                                                              *
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>%        So Many Computers , So Little Time ...                %
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