primer3-examples_2.4.0-2_all.deb


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Description

primer3-examples - tool to design flanking oligo nucleotides for DNA amplification (examples)

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename primer3-examples_2.4.0-2_all.deb
Package name primer3-examples
Package version 2.4.0
Package release 2
Package architecture all
Package type deb
Category universe/science
Homepage http://primer3.sourceforge.net
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 29.17 MB
Installed size 30.49 MB
Primer3 picks primers for Polymerase Chain Reactions (PCRs), considering as
criteria oligonucleotide melting temperature, size, GC content and
primer-dimer possibilities, PCR product size, positional constraints within
the source sequence, and 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.
This package contains example data to test the package.

Alternatives

Package Version Architecture Repository
primer3-examples_2.4.0-2_all.deb 2.4.0 all Ubuntu Universe
primer3-examples - - -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package primer3-examples_2.4.0-2_all.deb
Source Package primer3

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install primer3-examples deb package:
    # sudo apt-get install primer3-examples

Files

Path
/usr/share/doc/primer3-examples/changelog.Debian.gz
/usr/share/doc/primer3-examples/copyright
/usr/share/doc/primer3/examples/kmer_lists/homo_sapiens_11.list.gz
/usr/share/doc/primer3/examples/kmer_lists/homo_sapiens_16.list.gz
/usr/share/doc/primer3/examples/kmer_lists/mus_musculus_11.list.gz
/usr/share/doc/primer3/examples/kmer_lists/mus_musculus_16.list.gz
/usr/share/doc/primer3/examples/settings_files/primer3_v1_1_4_default_settings.txt
/usr/share/doc/primer3/examples/settings_files/primer3web_v0_4_0_default_settings.txt
/usr/share/doc/primer3/examples/settings_files/primer3web_v3_0_0_default_settings.txt.gz
/usr/share/doc/primer3/examples/settings_files/primer3web_v4_0_0_default_settings.txt.gz
/usr/share/doc/primer3/examples/src/humrep_and_simple.txt.gz
/usr/share/doc/primer3/examples/test/Makefile.gz
/usr/share/doc/primer3/examples/test/cmd_test3_output
/usr/share/doc/primer3/examples/test/cmd_test4_output
/usr/share/doc/primer3/examples/test/cmd_test5_output
/usr/share/doc/primer3/examples/test/cmdline_test.pl.gz
/usr/share/doc/primer3/examples/test/dpal_input.gz
/usr/share/doc/primer3/examples/test/dpal_long_input.gz
/usr/share/doc/primer3/examples/test/dpal_long_score_output
/usr/share/doc/primer3/examples/test/dpal_output.gz
/usr/share/doc/primer3/examples/test/dpal_score_output
/usr/share/doc/primer3/examples/test/dpal_test.pl.gz
/usr/share/doc/primer3/examples/test/dv_conc_vs_dntp_conc_input
/usr/share/doc/primer3/examples/test/dv_conc_vs_dntp_conc_output
/usr/share/doc/primer3/examples/test/long_seq_input.gz
/usr/share/doc/primer3/examples/test/long_seq_output.gz
/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl
/usr/share/doc/primer3/examples/test/masker.fna
/usr/share/doc/primer3/examples/test/masker_input
/usr/share/doc/primer3/examples/test/masker_output.gz
/usr/share/doc/primer3/examples/test/masker_test.pl.gz
/usr/share/doc/primer3/examples/test/not_for_production.lib.gz
/usr/share/doc/primer3/examples/test/not_for_production_Ns.lib.gz
/usr/share/doc/primer3/examples/test/not_for_production_Xs.lib.gz
/usr/share/doc/primer3/examples/test/oligotm.txt
/usr/share/doc/primer3/examples/test/oligotm_test.pl.gz
/usr/share/doc/primer3/examples/test/p3-tmpl-mispriming_input.gz
/usr/share/doc/primer3/examples/test/p3-tmpl-mispriming_output.gz
/usr/share/doc/primer3/examples/test/p3_3_prime_0_input.gz
/usr/share/doc/primer3/examples/test/p3_3_prime_0_output.gz
/usr/share/doc/primer3/examples/test/p3_3_prime_n_input.gz
/usr/share/doc/primer3/examples/test/p3_3_prime_n_output.gz
/usr/share/doc/primer3/examples/test/p3test.pl.gz
/usr/share/doc/primer3/examples/test/primer1_input.gz
/usr/share/doc/primer3/examples/test/primer1_output.gz
/usr/share/doc/primer3/examples/test/primer1_th_input.gz
/usr/share/doc/primer3/examples/test/primer1_th_output.gz
/usr/share/doc/primer3/examples/test/primer3_io_translator.pl.gz
/usr/share/doc/primer3/examples/test/primer3_v1_1_4_default_settings_input
/usr/share/doc/primer3/examples/test/primer3_v1_1_4_default_settings_output.gz
/usr/share/doc/primer3/examples/test/primer3web_v0_4_0_default_settings_input
/usr/share/doc/primer3/examples/test/primer3web_v0_4_0_default_settings_output.gz
/usr/share/doc/primer3/examples/test/primer3web_v3_0_0_default_settings_input
/usr/share/doc/primer3/examples/test/primer3web_v3_0_0_default_settings_output.gz
/usr/share/doc/primer3/examples/test/primer3web_v4_0_0_default_settings_input
/usr/share/doc/primer3/examples/test/primer3web_v4_0_0_default_settings_output.gz
/usr/share/doc/primer3/examples/test/primer_all_settingsfiles_input
/usr/share/doc/primer3/examples/test/primer_all_settingsfiles_output.gz
/usr/share/doc/primer3/examples/test/primer_boundary1_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_boundary1_input.gz
/usr/share/doc/primer3/examples/test/primer_boundary1_output.gz
/usr/share/doc/primer3/examples/test/primer_boundary_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_boundary_input.gz
/usr/share/doc/primer3/examples/test/primer_boundary_output.gz
/usr/share/doc/primer3/examples/test/primer_check_input.gz
/usr/share/doc/primer3/examples/test/primer_check_output.gz
/usr/share/doc/primer3/examples/test/primer_end_pathology_input
/usr/share/doc/primer3/examples/test/primer_end_pathology_output.gz
/usr/share/doc/primer3/examples/test/primer_first_base_index_input.gz
/usr/share/doc/primer3/examples/test/primer_first_base_index_output.gz
/usr/share/doc/primer3/examples/test/primer_gc_end_input.gz
/usr/share/doc/primer3/examples/test/primer_gc_end_output.gz
/usr/share/doc/primer3/examples/test/primer_high_gc_load_set.set
/usr/share/doc/primer3/examples/test/primer_high_gc_load_set_input
/usr/share/doc/primer3/examples/test/primer_high_gc_load_set_output.gz
/usr/share/doc/primer3/examples/test/primer_high_tm_load_set.set
/usr/share/doc/primer3/examples/test/primer_high_tm_load_set_input
/usr/share/doc/primer3/examples/test/primer_high_tm_load_set_output.gz
/usr/share/doc/primer3/examples/test/primer_human_input.gz
/usr/share/doc/primer3/examples/test/primer_human_output.gz
/usr/share/doc/primer3/examples/test/primer_input.gz
/usr/share/doc/primer3/examples/test/primer_internal1_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_internal1_input.gz
/usr/share/doc/primer3/examples/test/primer_internal1_output.gz
/usr/share/doc/primer3/examples/test/primer_internal_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_internal_input.gz
/usr/share/doc/primer3/examples/test/primer_internal_output.gz
/usr/share/doc/primer3/examples/test/primer_lib_amb_codes_input.gz
/usr/share/doc/primer3/examples/test/primer_lib_amb_codes_output.gz
/usr/share/doc/primer3/examples/test/primer_masker_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_masker_input.gz
/usr/share/doc/primer3/examples/test/primer_masker_output.gz
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary1_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary1_input
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary1_output.gz
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary2_formatted_output
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary2_input
/usr/share/doc/primer3/examples/test/primer_mispriming_boundary2_output
/usr/share/doc/primer3/examples/test/primer_mispriming_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_mispriming_input
/usr/share/doc/primer3/examples/test/primer_mispriming_long_lib_input
/usr/share/doc/primer3/examples/test/primer_mispriming_long_lib_output
/usr/share/doc/primer3/examples/test/primer_mispriming_output.gz
/usr/share/doc/primer3/examples/test/primer_mispriming_th_input
/usr/share/doc/primer3/examples/test/primer_mispriming_th_output.gz
/usr/share/doc/primer3/examples/test/primer_must_match_input.gz
/usr/share/doc/primer3/examples/test/primer_must_match_output.gz
/usr/share/doc/primer3/examples/test/primer_must_overlap_point_input.gz
/usr/share/doc/primer3/examples/test/primer_must_overlap_point_output.gz
/usr/share/doc/primer3/examples/test/primer_must_use_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_must_use_input.gz
/usr/share/doc/primer3/examples/test/primer_must_use_op_input.gz
/usr/share/doc/primer3/examples/test/primer_must_use_output.gz
/usr/share/doc/primer3/examples/test/primer_must_use_th_input.gz
/usr/share/doc/primer3/examples/test/primer_must_use_th_output.gz
/usr/share/doc/primer3/examples/test/primer_new_tasks_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_new_tasks_input.gz
/usr/share/doc/primer3/examples/test/primer_new_tasks_output.gz
/usr/share/doc/primer3/examples/test/primer_new_tasks_th_input.gz
/usr/share/doc/primer3/examples/test/primer_new_tasks_th_output.gz
/usr/share/doc/primer3/examples/test/primer_num_best_input.gz
/usr/share/doc/primer3/examples/test/primer_num_best_output.gz
/usr/share/doc/primer3/examples/test/primer_obj_fn_input.gz
/usr/share/doc/primer3/examples/test/primer_obj_fn_output.gz
/usr/share/doc/primer3/examples/test/primer_ok_regions2_input.gz
/usr/share/doc/primer3/examples/test/primer_ok_regions2_output.gz
/usr/share/doc/primer3/examples/test/primer_ok_regions_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_ok_regions_input
/usr/share/doc/primer3/examples/test/primer_ok_regions_output.gz
/usr/share/doc/primer3/examples/test/primer_output.gz
/usr/share/doc/primer3/examples/test/primer_overlap_junction_input
/usr/share/doc/primer3/examples/test/primer_overlap_junction_output.gz
/usr/share/doc/primer3/examples/test/primer_position_penalty_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_position_penalty_input.gz
/usr/share/doc/primer3/examples/test/primer_position_penalty_output.gz
/usr/share/doc/primer3/examples/test/primer_quality_boundary_input.gz
/usr/share/doc/primer3/examples/test/primer_quality_boundary_output.gz
/usr/share/doc/primer3/examples/test/primer_rat_input.gz
/usr/share/doc/primer3/examples/test/primer_rat_output.gz
/usr/share/doc/primer3/examples/test/primer_renewed_tasks_input
/usr/share/doc/primer3/examples/test/primer_renewed_tasks_output.gz
/usr/share/doc/primer3/examples/test/primer_repeat_boundary1_lib
/usr/share/doc/primer3/examples/test/primer_repeat_boundary2_lib
/usr/share/doc/primer3/examples/test/primer_repeat_long_lib.gz
/usr/share/doc/primer3/examples/test/primer_start_codon_input.gz
/usr/share/doc/primer3/examples/test/primer_start_codon_output.gz
/usr/share/doc/primer3/examples/test/primer_syntax_input.gz
/usr/share/doc/primer3/examples/test/primer_syntax_output.gz
/usr/share/doc/primer3/examples/test/primer_task_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_task_input
/usr/share/doc/primer3/examples/test/primer_task_output.gz
/usr/share/doc/primer3/examples/test/primer_task_th_input
/usr/share/doc/primer3/examples/test/primer_task_th_output.gz
/usr/share/doc/primer3/examples/test/primer_thal_args_input
/usr/share/doc/primer3/examples/test/primer_thal_args_output.gz
/usr/share/doc/primer3/examples/test/primer_thal_max_seq_error_input.gz
/usr/share/doc/primer3/examples/test/primer_thal_max_seq_error_output.gz
/usr/share/doc/primer3/examples/test/primer_thermod_align_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_thermod_align_input.gz
/usr/share/doc/primer3/examples/test/primer_thermod_align_output.gz
/usr/share/doc/primer3/examples/test/primer_three_prime_distance_input
/usr/share/doc/primer3/examples/test/primer_three_prime_distance_output.gz
/usr/share/doc/primer3/examples/test/primer_tm_lc_masking_formatted_output.gz
/usr/share/doc/primer3/examples/test/primer_tm_lc_masking_input
/usr/share/doc/primer3/examples/test/primer_tm_lc_masking_output.gz
/usr/share/doc/primer3/examples/test/repeat_lib1
/usr/share/doc/primer3/examples/test/repeat_lib2
/usr/share/doc/primer3/examples/test/repeat_lib3.gz
/usr/share/doc/primer3/examples/test/repeat_lib4
/usr/share/doc/primer3/examples/test/repeat_lib5.gz
/usr/share/doc/primer3/examples/test/repeat_lib6.gz
/usr/share/doc/primer3/examples/test/test_compl_error_input
/usr/share/doc/primer3/examples/test/test_compl_error_output
/usr/share/doc/primer3/examples/test/test_left_to_right_of_right_input
/usr/share/doc/primer3/examples/test/test_left_to_right_of_right_output
/usr/share/doc/primer3/examples/test/th-w-other-tasks-settings.txt
/usr/share/doc/primer3/examples/test/th-w-other-tasks_input.gz
/usr/share/doc/primer3/examples/test/th-w-other-tasks_output.gz
/usr/share/doc/primer3/examples/test/thal_input.gz
/usr/share/doc/primer3/examples/test/thal_long_input.gz
/usr/share/doc/primer3/examples/test/thal_long_temp_output
/usr/share/doc/primer3/examples/test/thal_output.gz
/usr/share/doc/primer3/examples/test/thal_temp_output.gz
/usr/share/doc/primer3/examples/test/thal_test.pl.gz
/usr/share/doc/primer3/examples/test/vgrep.pl
/usr/share/doc/primer3/examples/test/primer1_list_last/AGAG.for.gz
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/usr/share/doc/primer3/examples/test/primer3_config/stack.ds
/usr/share/doc/primer3/examples/test/primer3_config/stackmm.dh
/usr/share/doc/primer3/examples/test/primer3_config/stackmm.ds
/usr/share/doc/primer3/examples/test/primer3_config/tetraloop.dh
/usr/share/doc/primer3/examples/test/primer3_config/tetraloop.ds
/usr/share/doc/primer3/examples/test/primer3_config/triloop.dh
/usr/share/doc/primer3/examples/test/primer3_config/triloop.ds
/usr/share/doc/primer3/examples/test/primer3_config/tstack.dh
/usr/share/doc/primer3/examples/test/primer3_config/tstack2.dh
/usr/share/doc/primer3/examples/test/primer3_config/tstack2.ds
/usr/share/doc/primer3/examples/test/primer3_config/tstack_tm_inf.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/dangle_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/dangle_i.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/loops_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/loops_i.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/stack_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/stack_i.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/stackmm_i_mm.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/stackmm_i_mm.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/tetraloop_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/tetraloop_i.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/triloop_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/triloop_i.ds
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/tstack2_i.dh
/usr/share/doc/primer3/examples/test/primer3_config/interpretations/tstack2_i.ds
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Changelog

2018-05-28 - Liubov Chuprikova <chuprikovalv@gmail.com>
primer3 (2.4.0-2) unstable; urgency=medium
[ Liubov Chuprikova ]
* Team upload.
* Skip tests that fail on big endian
Closes: #890993
* Added d/README.source with explanation why some tests are skipped
* debian/patches/p3test_fix_exit_status.patch: Fix test to show correct exit
status
[ Andreas Tille ]
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
2018-02-21 - Andreas Tille <tille@debian.org>
primer3 (2.4.0-1) unstable; urgency=medium
* New upstream version
* Secure URI in watch file
* Standards-Version: 4.1.3
* debhelper 11
2017-09-14 - Steffen Moeller <moeller@debian.org>
primer3 (2.3.7-5) unstable; urgency=medium
* d/upstream/metadata:
- Added references to registries
- yamllint cleanliness
2017-08-26 - Andreas Tille <tille@debian.org>
primer3 (2.3.7-4) unstable; urgency=medium
* Fix build with gcc-7
Closes: #853621
* Standards-Version: 4.1.0 (no changes needed)
* d/rules: use DEB_SOURCE
* hardening=+all
2017-01-13 - Andreas Tille <tille@debian.org>
primer3 (2.3.7-3) unstable; urgency=medium
[ Andreas Tille ]
* debhelper 10
* d/watch: version=4
[ Helmut Grohne ]
* Fix FTCBFS: Pass CXX as CPP (Closes: #851230)
2016-06-27 - Canberk Koç <canberkkoc@gmail.com>
primer3 (2.3.7-2) unstable; urgency=medium
* Team Upload
[ Andreas Tille ]
* Moved packaging from SVN to Git
* cme fix dpkg-control
* better hardening
* split example data for test into separate arch all package
* add lintian override for empty directories
[ Canberk Koç ]
* Autopkgtest added
* debian/rules:
- added dh_clean to override_dh_auto_test section
- sed perl interpreter path
2016-03-10 - Andreas Tille <tille@debian.org>
primer3 (2.3.7-1) unstable; urgency=medium
* New upstream version
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
2013-12-19 - Andreas Tille <tille@debian.org>
primer3 (2.3.6-1) unstable; urgency=low
[ Charles Plessy ]
* New upstream release.
* Install configuration files in /etc (first step to fix bug 702693).
* Normalised debian/control with config-model-edit.
* Use canonical VCS URLs.
[ Andreas Tille ]
* Fix watch file
* replace cdbs by dh
* debian/patches/hardening.patch: Propagate hardening options
* Standards-Version: 3.9.5 (no changes needed)
* debian/patches/primer_thermodynamic_parameters_path_2_etc.patch:
Make sure config files will be searched for in /etc/primer3_config/
instead of /opt/primer3_config/
Closes: #702693
* Verified that new upstream
Closes: #716151, #716213 
* New executable: ntthal (including manpage)
* Removed *.xml variants of manpages to reduce redundancy
2013-02-05 - Andreas Tille <tille@debian.org>
primer3 (2.3.5-1) unstable; urgency=low
New upstream release.
[ Andreas Tille ]
* debian/upstream:
- Remove duplicated entry for PMID
- Added Volume, fixed Number
- Added URL+eprint
* debian/control:
- Removed DM-Upload-Allowed
- Standards-Version: 3.9.4 (no changes needed)
* debhelper 9 (control+compat)
* debian/copyright: PD License should be avoided - bumped packaging
to same license as program itself
2012-03-22 - Charles Plessy <plessy@debian.org>
primer3 (2.3.2-1) unstable; urgency=low
* New upstream release changing some default values.
* Refreshed debian/copyright to machine-readable format version 1.0.
Note that the license of Primer3 version 2.x changed to the GPLv2 or higher.
* Spellchecked manual pages (Closes: #650477, thanks to A. Costa).
* Using Debhelper 8 (debian/control, debian/compat).
* Renamed debian/README.Debian debian/README.test as it is all about tests.
* Conforms to Policy 3.9.3 (debian/control, no other changes needed).

See Also

Package Description
primer3_2.4.0-2_amd64.deb tool to design flanking oligo nucleotides for DNA amplification
primesieve-bin_7.3+ds-1ubuntu1_amd64.deb fast prime number generator C/C++ library -- bin
primesieve-doc_7.3+ds-1ubuntu1_all.deb fast prime number generator C/C++ library -- doc
primesieve_7.3+ds-1ubuntu1_amd64.deb fast prime number generator C/C++ library
primrose_6+dfsg1-4_amd64.deb compelling tile-placement puzzle game
primus-libs_0~20150328-7_amd64.deb Shared libraries for primus
primus_0~20150328-7_amd64.deb client-side GPU offloading for NVIDIA Optimus
princeprocessor_0.22-1_amd64.deb standalone password candidate generator using the PRINCE algorithm
print-manager_18.12.3-0ubuntu1_amd64.deb printer configuration and monitoring tools
printemf_1.0.11-2ubuntu1_amd64.deb Enhanced Metafile library (executable)
printer-driver-all-enforce_0.20170124_all.deb printer drivers metapackage - enforcing version
printer-driver-all_0.20170124_all.deb printer drivers metapackage
printer-driver-c2050_0.3b-8_amd64.deb printer driver for Lexmark 2050 Color Jetprinter
printer-driver-cjet_0.8.9-7_amd64.deb printer driver for Canon LBP laser printers
printer-driver-cups-pdf_3.0.1-5_amd64.deb printer driver for PDF writing via CUPS
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