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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.
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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. | ||
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Primer3 picks primers for PCR reactions, considering as criteria: o | ||
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- 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. | ||
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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. | ||
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Whitehead Institute for Biomedical Research provides a basic web-based | ||
front end to primer3 named primer3web at http://fokker.wi.mit.edu/ | ||
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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 |
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# $NetBSD: Makefile,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $ | ||
# | ||
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VERS= 2.2.3 | ||
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DISTNAME= primer3-${VERS} | ||
CATEGORIES= biology | ||
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=primer3/} | ||
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MAINTAINER= pkgsrc-users@NetBSD.org | ||
HOMEPAGE= http://primer3.sourceforge.net/ | ||
COMMENT= Design PCR primers | ||
LICENSE= gnu-gpl-v2 | ||
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PKG_DESTDIR_SUPPORT= user-destdir | ||
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USE_LANGUAGES= c c++ | ||
USE_TOOLS+= gmake | ||
BUILD_DIRS= src | ||
NO_CONFIGURE= yes | ||
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BINFILES+= long_seq_tm_test ntdpal ntthal oligotm primer3_core | ||
DOCFILES+= primer3_manual.htm primer3_v1_1_4_default_settings.txt | ||
DOCFILES+= primer3web_v0_4_0_default_settings.txt example | ||
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BINDIR= ${PREFIX}/bin | ||
DOCDIR= ${PREFIX}/share/doc/primer3 | ||
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INSTALLATION_DIRS+= ${BINDIR} ${DOCDIR} | ||
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do-install: | ||
.for f in ${BINFILES} | ||
${INSTALL_DATA} ${WRKSRC}/src/${f} ${DESTDIR}${BINDIR} | ||
.endfor | ||
.for f in ${DOCFILES} | ||
${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${DOCDIR} | ||
.endfor | ||
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.include "../../mk/bsd.pkg.mk" |
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@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $ | ||
bin/long_seq_tm_test | ||
bin/ntdpal | ||
bin/ntthal | ||
bin/oligotm | ||
bin/primer3_core | ||
share/doc/primer3/primer3_manual.htm | ||
share/doc/primer3/primer3_v1_1_4_default_settings.txt | ||
share/doc/primer3/primer3web_v0_4_0_default_settings.txt | ||
share/doc/primer3/example |
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$NetBSD: distinfo,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $ | ||
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SHA1 (primer3-2.2.3.tar.gz) = 20c6a00455b86a5712c1e297930f2624fca45881 | ||
RMD160 (primer3-2.2.3.tar.gz) = 040b41649f5bfc17214502b2ba5e98d1a5afd73f | ||
Size (primer3-2.2.3.tar.gz) = 2284282 bytes | ||
SHA1 (patch-src_primer3__boulder__main.c) = a9228eb3f8f1969a6bc332f828db2def7cf00005 |
15 changes: 15 additions & 0 deletions
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biology/primer3/patches/patch-src_primer3__boulder__main.c
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$NetBSD: patch-src_primer3__boulder__main.c,v 1.1.1.1 2011/10/31 21:25:57 brook Exp $ | ||
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getopt_long_only is not very portable; use getopt_long instead. | ||
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--- src/primer3_boulder_main.c.orig 2010-07-08 17:58:25.000000000 +0000 | ||
+++ src/primer3_boulder_main.c | ||
@@ -133,7 +133,7 @@ main(int argc, char *argv[]) | ||
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/* Read in the flags provided with the program call */ | ||
opterr = 0; | ||
- while ((opt = getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { | ||
+ while ((opt = getopt_long(argc, argv, "", long_options, &option_index)) != -1) { | ||
switch (opt) { | ||
case 'a': | ||
about = 1; |