primer3_2.3.6-1_amd64.deb


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Description

primer3 - Tool to design flanking oligo nucleotides for DNA amplification

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe amd64
Package name primer3
Package version 2.3.6
Package release 1
Package architecture amd64
Package type deb
Installed size 673 B
Download size 164.94 KB
Official Mirror archive.ubuntu.com
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.

Alternatives

Package Version Architecture Repository
primer3_2.3.6-1_i386.deb 2.3.6 i386 Ubuntu Universe
primer3 - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:4.1.1
libstdc++6 >= 4.1.1

Download

Type URL
Binary Package primer3_2.3.6-1_amd64.deb
Source Package primer3

Install Howto

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

Files

Path
/etc/primer3_config/dangle.dh
/etc/primer3_config/dangle.ds
/etc/primer3_config/loops.dh
/etc/primer3_config/loops.ds
/etc/primer3_config/stack.dh
/etc/primer3_config/stack.ds
/etc/primer3_config/stackmm.dh
/etc/primer3_config/stackmm.ds
/etc/primer3_config/tetraloop.dh
/etc/primer3_config/tetraloop.ds
/etc/primer3_config/triloop.dh
/etc/primer3_config/triloop.ds
/etc/primer3_config/tstack.dh
/etc/primer3_config/tstack2.dh
/etc/primer3_config/tstack2.ds
/etc/primer3_config/tstack_tm_inf.ds
/etc/primer3_config/interpretations/dangle_i.dh
/etc/primer3_config/interpretations/dangle_i.ds
/etc/primer3_config/interpretations/loops_i.dh
/etc/primer3_config/interpretations/loops_i.ds
/etc/primer3_config/interpretations/stack_i.dh
/etc/primer3_config/interpretations/stack_i.ds
/etc/primer3_config/interpretations/stackmm_i_mm.dh
/etc/primer3_config/interpretations/stackmm_i_mm.ds
/etc/primer3_config/interpretations/tetraloop_i.dh
/etc/primer3_config/interpretations/tetraloop_i.ds
/etc/primer3_config/interpretations/triloop_i.dh
/etc/primer3_config/interpretations/triloop_i.ds
/etc/primer3_config/interpretations/tstack2_i.dh
/etc/primer3_config/interpretations/tstack2_i.ds
/etc/primer3_config/interpretations/tstack_i.dh
/etc/primer3_config/interpretations/tstack_i.ds
/etc/primer3_config/interpretations/tstack_tm_inf_i.dh
/etc/primer3_config/interpretations/tstack_tm_inf_i.ds
/usr/bin/ntdpal
/usr/bin/ntthal
/usr/bin/oligotm
/usr/bin/primer3_core
/usr/share/doc-base/primer3-manual
/usr/share/doc/primer3/README.test
/usr/share/doc/primer3/changelog.Debian.gz
/usr/share/doc/primer3/copyright
/usr/share/doc/primer3/primer3_manual.htm
/usr/share/doc/primer3/release_notes.txt.gz
/usr/share/doc/primer3/examples/example
/usr/share/man/man1/ntdpal.1.gz
/usr/share/man/man1/ntthal.1.gz
/usr/share/man/man1/oligotm.1.gz
/usr/share/man/man1/primer3_core.1.gz

Changelog

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).
2010-11-17 - Andreas Tille <tille@debian.org>
primer3 (2.2.3-1) unstable; urgency=low
* New upstream version
* debian/primer3.docs: s/README.txt/primer3_manual.htm/
* debian/compat: 7
* debian/control:
- Build-Depends: debhelper (>= 7)
- Standards-Version: 3.9.1 (no changes needed
* debian/source/format: 3.0 (quilt)
* debian/README.source
* debian/primer3.doc-base
2009-05-23 - David Paleino <d.paleino@gmail.com>
primer3 (1.1.4-2) UNRELEASED; urgency=low
[ David Paleino ]
* Removed myself from Uploaders
[ Charles Plessy ]
* Documented informations in ‘debian/upstream-metadata.yaml’.
* Removed mention of the bibliographic reference and the webservice in
‘debian/control’.
2008-05-09 - Charles Plessy <plessy@debian.org>
primer3 (1.1.4-1) unstable; urgency=low
* New upstream release (No changes on Linux systems).
* Updated my email address (debian/control, debian/copyright, manpages).
* Updated the manpages:
- using DocBook 4.5
- incremented Primer3 version to 1.1.4
2008-02-25 - Charles Plessy <charles-debian-nospam@plessy.org>
primer3 (1.1.3-1) unstable; urgency=low
[ Charles Plessy ]
* New upstream version:
- 1.1.3: Corrected static buffer overflow errors in
boulder_print_pairs() and boulder_print_oligos() in primer3_main.c.
- 1.1.2: Updates to dpal.c so that no error forces an exit.
Adpatation in primer3_main.c and ntdpal_main.c to
updated error handling in dpal().
Arranged for primer3_main.c align() to check for
and circumvent local alignments to "targets" < 3 nucleotides
long, and added tests for this condition.
Comment and code readability updates in dpal.h and dpal.c
* Moved the Homepage: field out from the package's description.
* debian/control: updated Steffen's email address.
* debian/*.1.xml: corrected the headers of the sources of manpages.
* debian/rules: converted to CDBS.
[ David Paleino ]
* debian/ntdpal.1, debian/primer3_core.1 and debian/oligotm.1
added - manpages are statically built now
* debian/control:
- B-D updated
- added myself to Uploaders
* Updated to Standards-Version 3.7.3 (no changes needed)

See Also

Package Description
primesieve-bin_5.6.0+ds-1_amd64.deb fast prime number generator C/C++ library -- bin
primesieve-doc_5.6.0+ds-1_all.deb fast prime number generator C/C++ library -- doc
primesieve_5.6.0+ds-1_amd64.deb fast prime number generator C/C++ library
primrose_6+dfsg1-3_amd64.deb compelling tile-placement puzzle game
primus-libs_0~20150328-1_amd64.deb Shared libraries for primus
primus_0~20150328-1_amd64.deb client-side GPU offloading for NVIDIA Optimus
print-manager_15.12.3-0ubuntu1_amd64.deb printer configuration and monitoring tools
printer-driver-all-enforce_0.20140714build1_all.deb printer drivers metapackage - enforcing version
printer-driver-all_0.20140714build1_all.deb printer drivers metapackage
printer-driver-c2050_0.3b-6_amd64.deb printer driver for Lexmark 2050 Color Jetprinter
printer-driver-cjet_0.8.9-6_amd64.deb printer driver for Canon LBP laser printers
printer-driver-cups-pdf_2.6.1-21_amd64.deb printer driver for PDF writing via CUPS
printer-driver-dymo_1.4.0-5_amd64.deb printer driver for DYMO label printers
printer-driver-escpr_1.6.3-2_amd64.deb printer driver for Epson Inkjet that use ESC/P-R
printer-driver-indexbraille_1.2.2-1_amd64.deb CUPS printing to Index Braille printers
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