ncbi-epcr_2.3.12-1-7_amd64.deb


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Description

ncbi-epcr - Tool to test a DNA sequence for the presence of sequence tagged sites

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename ncbi-epcr_2.3.12-1-7_amd64.deb
Package name ncbi-epcr
Package version 2.3.12
Package release 1-7
Package architecture amd64
Package type deb
Category universe/science
Homepage https://www.ncbi.nlm.nih.gov/tools/epcr/
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 120.39 KB
Installed size 467.00 KB
Electronic PCR (e-PCR) is computational procedure that is used to identify
sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential
STSs in DNA sequences by searching for subsequences that closely match the
PCR primers and have the correct order, orientation, and spacing that could
represent the PCR primers used to generate known STSs.
The new version of e-PCR implements a fuzzy matching strategy. To reduce
likelihood that a true STS will be missed due to mismatches, multiple
discontiguous words may be used instead of a single exact word. Each of this
word has groups of significant positions separated by 'wildcard' positions
that are not required to match. In addition, it is also possible to allow
gaps in the primer alignments.
The main motivation for implementing reverse searching (called Reverse e-PCR)
was to make it feasible to search the human genome sequence and other large
genomes. The new version of e-PCR provides a search mode using a query
sequence against a sequence database.
This program is retired upstream and it is suggested to use Primer-Blast
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
instead.

Alternatives

Package Version Architecture Repository
ncbi-epcr_2.3.12-1-7_i386.deb 2.3.12 i386 Ubuntu Universe
ncbi-epcr - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:3.0
libstdc++6 >= 5.2

Download

Type URL
Mirror archive.ubuntu.com
Binary Package ncbi-epcr_2.3.12-1-7_amd64.deb
Source Package epcr

Install Howto

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

Files

Path
/usr/bin/e-PCR
/usr/bin/fahash
/usr/bin/famap
/usr/bin/re-PCR
/usr/share/doc/ncbi-epcr/README.html
/usr/share/doc/ncbi-epcr/README.txt.gz
/usr/share/doc/ncbi-epcr/RETIRED_README.txt
/usr/share/doc/ncbi-epcr/changelog.Debian.gz
/usr/share/doc/ncbi-epcr/copyright
/usr/share/man/man1/e-PCR.1.gz
/usr/share/man/man1/fahash.1.gz
/usr/share/man/man1/famap.1.gz
/usr/share/man/man1/re-PCR.1.gz

Changelog

2019-02-13 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-7) unstable; urgency=medium
[ Do Thanh Trung ]
* Enable cross building
Closes: #922192
[ Andreas Tille ]
* Secure URI for homepage
* Standards-Version: 4.3.0
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
* Drop non-functional autopkgtest template
2018-10-14 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-6) unstable; urgency=medium
[ Andreas Tille ]
* debian/upstream/metadata
- Add registry data
- remove wrong and redundat information
[ Manas Kashyap ]
* VCS updated
* Debhelper bumped
* Standard version updated
[ Andreas Tille ]
* Versioned Build-Depends: debhelper (>= 11~) to enable easy backports
* Fix spelling
* Do not parse d/changelog
2017-09-27 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-5) unstable; urgency=medium
* Moved packaging from SVN to Git
* Add upstream note that epcr is retired
* Reflect in watch file that there will be no new versions
* Add note about retired program to long description
* Standards-Version: 4.1.0 (no changes needed)
2016-12-17 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-4) unstable; urgency=medium
* d/watch: version=4
* debhelper 10
* cme fix dpkg-control
* hardening=+all
2015-12-21 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-3) unstable; urgency=medium
* new homepage
* cme fix dpkg-control
* Fix Mayhem issue
Closes: #715850
2014-08-23 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-2) unstable; urgency=low
[ Charles Plessy ]
* Normalised debian/control with ‘config-model-edit‘.
This also removed the obsolete DM-Upload-Allowed field.
* Conforms with Policy 3.9.4.
[ Andreas Tille ]
* cme fix dpkg-control
* Moved debian/upstream to debian/upstream/metapackages
2012-04-25 - Andreas Tille <tille@debian.org>
epcr (2.3.12-1-1) unstable; urgency=low
* New upstream version that has applied debian/patches/gcc-4.7.patch
(so this patch was removed)
* debian/copyright: Add Upstream-Name & Upstream-Contact
* debian/control: SVN dir was renamed from ncbi-epcr to epcr
* debian/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
hardening flags
* debian/rules:
- do not specify fixed version strings but rather obtain these
via dpkg-parsechangelog
- Enable hardening flags
2012-04-22 - Andreas Tille <tille@debian.org>
epcr (2.3.12-3) unstable; urgency=low
[ A. Costa ]
* Corrected typos in manpages (Closes: #650476).
[ Charles Plessy ]
* Lifted debian/copyright to latest DEP 5 draft.
[ Andreas Tille ]
* debian/upstream: Took over references from debian/reference
and debian/README.Debian
* debian/control:
- Standards-Version: 3.9.3
- Fixed Vcs fields
* debian/{control,rules}: Removed explicite dependency from quilt
* debian/patches/gcc-4.7.patch: Add missing include to build using
gcc-4.7
Closes: #667156
* debian/copyright: Fix DEP5 and verify using
cme fix dpkg-copyright
* debhelper 9 (control+compat)
2011-02-22 - Andreas Tille <tille@debian.org>
epcr (2.3.12-2) unstable; urgency=low
* debian/source/format: 3.0 (quilt)
* Standards-Version: 3.9.1 (no changes needed)
* debian/rules: Implementation of upstream build systems seems to
be simpler with short dh rules file
* debian/patches: Ensure Build options will be propagated properly
Closes: 614482
2009-07-02 - Charles Plessy <plessy@debian.org>
epcr (2.3.12-1) unstable; urgency=low
* New upstream release buildable with GCC 4.4 (Closes: #504849)
* Version number updated in debian/rules.
* debian/copyright refreshed to my latest exploration of the
machine-readable format.
* Added a BibTeX reference in debian/reference.

See Also

Package Description
ncbi-rrna-data_6.1.20170106-6_all.deb large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-seg_0.0.20000620-5_amd64.deb tool to mask segments of low compositional complexity in amino acid sequences
ncbi-tools-bin_6.1.20170106-6_amd64.deb NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11_6.1.20170106-6_amd64.deb NCBI libraries for biology applications (X-based utilities)
ncc_2.8-2.1build1_amd64.deb C source code analyzer
ncdt_2.1-4_amd64.deb Display directory tree
ncdu_1.13-1_amd64.deb ncurses disk usage viewer
ncftp_3.2.5-2.1_amd64.deb User-friendly and well-featured FTP client
ncl-ncarg_6.5.0-2_amd64.deb NCAR Command Language and NCAR graphics
ncl-tools_2.1.21+git20180827.c71b264-2_amd64.deb tools to deal with NEXUS files
ncmpc-lyrics_0.33-2_all.deb ncurses-based audio player (lyrics plugins)
ncmpc_0.33-2_amd64.deb ncurses-based audio player
ncmpcpp_0.8.2-0.1build1_amd64.deb ncurses-based client for the Music Player Daemon (MPD)
nco_4.7.9-1_amd64.deb Command-line operators to analyze netCDF files
ncoils_2002-7_amd64.deb coiled coil secondary structure prediction
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