primer3_2.3.6-1_amd64.deb


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Description

primer3 - Tool to design flanking oligo nucleotides for DNA amplification

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

    Download

    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

    • /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)

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