New upstream version 2.4.0

# Compiled Object files

*.o

# Compiled Static libraries

*.a

# Executables

src/long_seq_tm_test

src/ntdpal

src/ntthal

src/oligotm

src/primer3_core

src/primer3_masker

src/*.exe

# Temporary Test Files

test/primer1_list_tmp/*

test/primer1_th_list_tmp/*

test/primer_list_tmp/*

test/th-w-other-tasks_list_tmp/*

test/*.err

test/*.tmp

test/*.tmp2

test/*.valg

test/*.vg

test/primer_global_err/*.tmp

test/primer_global_err/*.tmp2

test/primer_global_err/*.valg

test/primer_global_err/*.vg

# Individual Test Files

test/hyb_probe_only.for

test/hyb_probe_only.int

test/left_only.for

test/pcr_primers.for

test/pcr_primers.rev

test/pcr_primers_and_io.for

test/pcr_primers_and_io.int

test/pcr_primers_and_io.rev

test/right_only.for

test/right_only.rev

test/syntax01.for

test/syntax01.int

test/syntax01.rev

test/syntax02.for

test/syntax02.int

test/syntax02.rev

test/syntax03.for

test/syntax03.int

test/syntax03.rev

test/syntax04.for

test/syntax04.int

test/syntax04.rev

test/syntax07.for

test/syntax07.int

test/syntax07.rev

test/syntax09.for

test/syntax09.int

test/syntax09.rev

test/syntax10.for

test/syntax10.int

test/syntax10.rev

.DS_Store

Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3").

From mispriming libraries to sequence quality data to the generation of internal

oligos, primer3 does it. C&perl.

Installing

----------

`sudo apt-get install -y build-essential g++ cmake git-all`

`git clone https://github.com/primer3-org/primer3.git primer3`

`cd primer3/src`

`make`

`make test`

Run Primer3

-----------

`./primer3_core ../example`

Read the complete Primer3 manual

--------------------------------

[Primer3 Manual](http://primer3.org/primer3_manual.htm)

or see /src/primer3_manual.htm

#!/usr/bin/perl

# ======================================================================

# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2010,

#  2011,2012,2016

# Whitehead Institute for Biomedical Research, Steve Rozen, 

# Andreas Untergasser and Helen Skaletsky

# All rights reserved.

# 

#   This file is part of the primer3 suite.

#

#   The primer3 suite is free software; you can redistribute it and/or

#   modify it under the terms of the GNU General Public License as

#   published by the Free Software Foundation; either version 2 of the

#   License, or (at your option) any later version.

#

#   This software is distributed in the hope that it will be useful,

#   but WITHOUT ANY WARRANTY; without even the implied warranty of

#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

#   GNU General Public License for more details.

#

#   You should have received a copy of the GNU General Public License

#   along with this file (file gpl-2.0.txt in the source distribution); if

#   not, write to the Free Software Foundation, Inc., 51 Franklin St,

#   Fifth Floor, Boston, MA 02110-1301 USA

# 

# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# ======================================================================

use warnings 'all';

use strict;

if (-d "test") {

    if (-d "test/primer_list_tmp") {

        print "Folder excists: test/primer_list_tmp\n";

    } else {

        mkdir "test/primer_list_tmp";

        print "Created folder: test/primer_list_tmp\n";

    }

    if (-d "test/primer1_list_tmp") {

        print "Folder excists: test/primer1_list_tmp\n";

    } else {

        mkdir "test/primer1_list_tmp";

        print "Created folder: test/primer1_list_tmp\n";

    }

    if (-d "test/primer1_th_list_tmp") {

        print "Folder excists: test/primer1_th_list_tmp\n";

    } else {

        mkdir "test/primer1_th_list_tmp";

        print "Created folder: test/primer1_th_list_tmp\n";

    }

    if (-d "test/th-w-other-tasks_list_tmp") {

        print "Folder excists: test/th-w-other-tasks_list_tmp\n";

    } else {

        mkdir "test/th-w-other-tasks_list_tmp";

        print "Created folder: test/th-w-other-tasks_list_tmp\n";

    }

}

else {

    print "Run this script in the Primer3 root folder\n";

}

SEQUENCE_ID=example

SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG

SEQUENCE_TARGET=37,21

PRIMER_TASK=pick_detection_primers

SEQUENCE_TEMPLATE=tattggtgaagcctcaggtagtgcagaatatgaaacttcaggatccagtgggcatgctactggtagtgctgccggccttacaggcattatggtggcaaagtcgacagagttta

PRIMER_TASK=generic

PRIMER_PICK_LEFT_PRIMER=1

PRIMER_PICK_INTERNAL_OLIGO=1

PRIMER_PICK_INTERNAL_OLIGO=0

PRIMER_PICK_RIGHT_PRIMER=1

PRIMER_OPT_SIZE=18

PRIMER_MIN_SIZE=15

PRIMER_MAX_SIZE=21

PRIMER_MAX_NS_ACCEPTED=1

PRIMER_PRODUCT_SIZE_RANGE=75-100

P3_FILE_FLAG=1

SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21

PRIMER_OPT_SIZE=20

PRIMER_MIN_SIZE=18

PRIMER_MAX_SIZE=22

PRIMER_PRODUCT_SIZE_RANGE=75-150

PRIMER_EXPLAIN_FLAG=1

=