./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


Required to build:
[pkgtools/cwrappers]

Master sites:

Filesize: 1628.489 KB

Version history: (Expand)

CVS history: (Expand)


   2023-08-02 21:20:20 by Nia Alarie | Files touched by this commit (30) 
Log message:
*: Mark packages that were originally identified as requiring
C++03 due to failing to build with a C++14 default compiler
with FORCE_CXX_STD instead of USE_LANGUAGES.
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2020-03-20 12:58:37 by Nia Alarie | Files touched by this commit (640) 
Log message:
*: Convert broken sourceforge HOMEPAGEs back to http
   2020-01-19 00:36:14 by Roland Illig | Files touched by this commit (3046) 
Log message:
all: migrate several HOMEPAGEs to https

pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
   2018-07-18 02:06:25 by Joerg Sonnenberger | Files touched by this commit (168) 
Log message:
Mark packages that require C++03 (or the GNU variants) if they fail with
C++14 default language.
   2018-01-01 23:30:04 by Roland Illig | Files touched by this commit (537) 
Log message:
Sort PLIST files.

Unsorted entries in PLIST files have generated a pkglint warning for at
least 12 years. Somewhat more recently, pkglint has learned to sort
PLIST files automatically. Since pkglint 5.4.23, the sorting is only
done in obvious, simple cases. These have been applied by running:

  pkglint -Cnone,PLIST -Wnone,plist-sort -r -F
   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.