pkg-descr

"Primer3 is a complete rewrite of the original PRIMER program
(Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric
Lander. See DIFFERENCES FROM EARLIER VERSIONS for a discussion
of how Primer3 differs from its predecessors, Primer 0.5 and
Primer v2.

Primer3 picks primers for PCR reactions, considering as criteria:

o oligonucleotide melting temperature, size, GC content,
and primer-dimer possibilities,
o PCR product size,
o positional constraints within the source sequence, and
o miscellaneous 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."
- from the README file

WWW: http://www-genome.wi.mit.edu/genome_software/other/primer3.html

--
Tony Maher

pkg-message

Copyright (c) 1996,1997,1998
Whitehead Institute for Biomedical Research. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. Redistributions of
source code must also reproduce this information in the source code itself.

2. If the program is modified, redistributions must include a notice
(in the same places as above) indicating that the redistributed program is
not identical to the version distributed by Whitehead Institute.

3. All advertising materials mentioning features or use of this
software must display the following acknowledgment:
This product includes software developed by the
Whitehead Institute for Biomedical Research.

4. The name of the Whitehead Institute may not be used to endorse or
promote products derived from this software without specific prior written
permission.

We also request that use of this software be cited in publications as

Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
Primer3. Code available at
http://www-genome.wi.mit.edu/genome_software/other/primer3.html

THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``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 WHITEHEAD INSTITUTE 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.

pkg-plist

bin/primer3
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%%PORTDOCS%%%%DOCSDIR%%/example
%%PORTDOCS%%%%EXAMPLESDIR%%/Makefile
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary1_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary2_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_long_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_formatted_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_output
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib2
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib3
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib4
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib5
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib6
%%PORTDOCS%%%%EXAMPLESDIR%%/vgrep.pl
%%DATADIR%%/COPYING.txt
@dirrm %%DATADIR%%
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%