xtandem-2015.12.15-1.82.x86_64.rpm


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Description

xtandem - Tool for protein identification from mass spectra

Property Value
Distribution openSUSE Tumbleweed
Repository Science all
Package name xtandem
Package version 2015.12.15
Package release 1.82
Package architecture x86_64
Package type rpm
Installed size 1.43 MB
Download size 504.21 KB
Official Mirror widehat.opensuse.org
X! Tandem open source is software that can match tandem mass spectra
with peptide sequences, in a process that has come to be known as protein
identification.
This software has a very simple, sophisticated application programming
interface (API): it simply takes an XML file of instructions on its
command line, and outputs the results into an XML file, which has been
specified in the input XML file. This format is used for all of the X!
series search engines, as well as the GPM and GPMDB.
Unlike some earlier generation search engines, all of the X! Series search
engines calculate statistical confidence (expectation values) for all of
the individual spectrum-to-sequence assignments. They also reassemble all
of the peptide assignments in a data set onto the known protein sequences
and assign the statistical confidence that this assembly and alignment
is non-random. Therefore, separate assembly and statistical analysis
software, e.g. PeptideProphet and ProteinProphet, do not need to be used.

Alternatives

Package Version Architecture Repository
xtandem-2015.12.15-1.82.i586.rpm 2015.12.15 i586 Science
xtandem - - -

Requires

Name Value
/usr/bin/perl -
libc.so.6(GLIBC_2.14)(64bit) -
libexpat.so.1()(64bit) -
libgcc_s.so.1()(64bit) -
libgcc_s.so.1(GCC_3.0)(64bit) -
libm.so.6()(64bit) -
libm.so.6(GLIBC_2.2.5)(64bit) -
libpthread.so.0()(64bit) -
libpthread.so.0(GLIBC_2.2.5)(64bit) -
libstdc++.so.6()(64bit) -
libstdc++.so.6(CXXABI_1.3)(64bit) -
libstdc++.so.6(CXXABI_1.3.8)(64bit) -
libstdc++.so.6(CXXABI_1.3.9)(64bit) -
libstdc++.so.6(GLIBCXX_3.4)(64bit) -
libstdc++.so.6(GLIBCXX_3.4.11)(64bit) -
libstdc++.so.6(GLIBCXX_3.4.20)(64bit) -
libstdc++.so.6(GLIBCXX_3.4.21)(64bit) -
libstdc++.so.6(GLIBCXX_3.4.9)(64bit) -
libz.so.1()(64bit) -

Provides

Name Value
xtandem = 2015.12.15-1.82
xtandem(x86-64) = 2015.12.15-1.82

Download

Type URL
Binary Package xtandem-2015.12.15-1.82.x86_64.rpm
Source Package xtandem-2015.12.15-1.82.src.rpm

Install Howto

  1. Add the Science repository:
    # zypper addrepo http://widehat.opensuse.org/opensuse/repositories/science/openSUSE_Tumbleweed/ science
  2. Install xtandem rpm package:
    # zypper install xtandem

Files

Path
/usr/bin/xtandem
/usr/bin/xtandem2mgf
/usr/share/man/man1/xtandem.1.gz
/usr/share/man/man1/xtandem2mgf.1.gz
/usr/share/xtandem/default_input.xml
/usr/share/xtandem/input.xml
/usr/share/xtandem/taxonomy.xml
/usr/share/xtandem/test_spectra.mgf
/usr/share/xtandem/xsl/tandem-input-style.xsl
/usr/share/xtandem/xsl/tandem-style.css
/usr/share/xtandem/xsl/tandem-style.xsl
/usr/share/xtandem/xsl/tandem2csv.xsl

Changelog

2016-05-28 - archie.cobbs@gmail.com
- Update to release 2015.12.15
2016-01-29 - archie.cobbs@gmail.com
- Handle mzML file RT times that are in seconds not minutes
2015-10-02 - archie.cobbs@gmail.com
- Fix error in previous upgrade wrt. decomp.patch
2015-10-02 - archie.cobbs@gmail.com
- Update to release 2015.04.01
2014-08-22 - archie@dellroad.org
- Fix segfault on exit when no spectra meet acceptance criteria
- Added patches:
* no-spectra-segfault.patch
2013-12-17 - archie@dellroad.org
- Add xtandem2mgf utility based on plibrary.pl from web site
- Remove database files as they are large and quickly obsolete
- added patches:
* plibrary.patch
2013-11-03 - archie@dellroad.org
- Update to release 2013-09-01
2013-08-07 - archie@dellroad.org
- Update to release 2013-06-15
2013-04-04 - archie@dellroad.org
- Update to release 2013-02-01
2013-03-27 - archie@dellroad.org
- Add support for zlib compressed data
- Update patch to fix compile warning

See Also

Package Description
xxhash-0.6.5-6.1.i586.rpm Non-cryptographic hash algorithm
xxhash-0.6.5-6.1.x86_64.rpm Non-cryptographic hash algorithm
xxhash-devel-0.6.5-6.1.i586.rpm Development files for xxHash - a non-cryptographic hash algorithm
xxhash-devel-0.6.5-6.1.x86_64.rpm Development files for xxHash - a non-cryptographic hash algorithm
xyconv-1.5-12.44.i586.rpm Command-line converter of files in formats supported by xylib
xyconv-1.5-12.44.x86_64.rpm Command-line converter of files in formats supported by xylib
xyconvert-1.5-12.44.i586.rpm GUI converter of files in formats supported by xylib
xyconvert-1.5-12.44.x86_64.rpm GUI converter of files in formats supported by xylib
xylib-devel-1.5-12.44.i586.rpm Development files for xylib
xylib-devel-1.5-12.44.x86_64.rpm Development files for xylib
xyscan-4.30-4.1.i586.rpm Data extractor for data points from graphical plots
xyscan-4.30-4.1.x86_64.rpm Data extractor for data points from graphical plots
xyscan-doc-4.30-4.1.noarch.rpm Documentation for xyscan
zipios-devel-2.1.1-2.16.i586.rpm Zipios++ Header Files
zipios-devel-2.1.1-2.16.x86_64.rpm Zipios++ Header Files
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