Installed
This software should be available with no extra configuration.
primer3-2.6.1
Primer3 picks primers for PCR reactions, considering as criteria:
- oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities,
- PCR product size,
- positional constraints within the source (template) sequence, and
- possibilities for ectopic priming (amplifying the wrong sequence)
- 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.
Manual
The primer3 manual can be found here.
Location and version
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$ which primer3_core
/local/cluster/bin/primer3_core
$ primer3_core -h 2>&1 | grep release
This is primer3 (libprimer3 release 2.6.1)
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help message
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$ primer3_core -h
Copyright (c) 1996-2022
Whitehead Institute for Biomedical Research, Steve Rozen
(http://purl.com/STEVEROZEN/), Andreas Untergasser and Helen Skaletsky
All rights reserved.
This file is part of the primer3 suite and libraries.
The primer3 suite and libraries are free software;
you can redistribute them and/or modify them 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 software (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.
USAGE: primer3_core [--format_output] [--default_version=1|--default_version=2] [--io_version=4] [--p3_settings_file=<file_path>] [--echo_settings_file] [--strict_tags] [--output=<file_path>] [--error=<file_path>] [input_file]
This is primer3 (libprimer3 release 2.6.1)
Input can also be provided on standard input.
For example:
$ primer3_core < my_input_file
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software ref: https://github.com/primer3-org/primer3
research ref: https://doi.org/10.1093/nar/gks596
research ref: https://doi.org/10.1093/bioinformatics/btm091