./biology/primer3, Design PCR primers

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Branch: CURRENT, Version: 2.3.6, Package name: primer3-2.3.6, Maintainer: pkgsrc-users

Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
in genetics and molecular biology. Primer3 can also design
hybridization probes and sequencing primers.

Primer3 picks primers for PCR reactions, considering as criteria: o

- oligonucleotide melting temperature, size, GC content, and
primer-dimer possibilities,
- PCR product size,
- positional constraints within the source (template) sequence,
- possibilities for ectopic priming (amplifying the wrong sequence), and
- many other constraints.

All of these criteria are user-specifiable as constraints, and some
are specifiable as terms in an objective function that characterizes
an optimal primer pair.

Whitehead Institute for Biomedical Research provides a basic web-based
front end to primer3 named primer3web at http://fokker.wi.mit.edu/

Wageningen University Laboratory of Bioinformatics provides a enhanced
web-based front end to primer3 named primer3plus at
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi


Master sites:

SHA1: 7dbd33a4e9c2a4fe06c74d6b83f8ff0f9ed1c49a
RMD160: 1cd48d0677303efd5ca0ce76ac46c04fd5f29b9c
Filesize: 1628.489 KB

Version history: (Expand)


CVS history: (Expand)


   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38)
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2015-01-31 07:21:39 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
Use INSTALL_PROGRAM for executables (instead of INSTALL_DATA).
   2015-01-31 07:18:43 by Makoto Fujiwara | Files touched by this commit (3) | Package updated
Log message:
Update 2.2.3 to 2.3.6
---------------------
ChangeLog unknown.
   2012-09-11 22:32:15 by Aleksej Saushev | Files touched by this commit (31)
Log message:
"user-destdir" is default these days
   2011-10-31 22:25:57 by Brook Milligan | Files touched by this commit (5) | Imported package
Log message:
Initial import of primer3.

Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction").  PCR is an essential and ubiquitous tool
in genetics and molecular biology.  Primer3 can also design
hybridization probes and sequencing primers.