tm-align_20120507-1_i386.deb


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Description

tm-align - structual alignment of proteins

Property Value
Distribution Debian 7 (Wheezy)
Repository Debian Main i386
Package name tm-align
Package version 20120507
Package release 1
Package architecture i386
Package type deb
Installed size 503 B
Download size 48.74 KB
Official Mirror ftp.br.debian.org
TM-align is a computer algorithm for protein structure alignment using
dynamic programming. The scoring is performed by the TM-score rotation
matrix. This is similar to the RMSD in that unaligned portions of the
structure influence the scoring less than the more structurally conserved
regions.

Alternatives

Package Version Architecture Repository
tm-align_20120507-1_amd64.deb 20120507 amd64 Debian Main
tm-align - - -

Requires

Name Value
libc6 >= 2.0
libgcc1 >= 1:4.1.1
libgfortran3 >= 4.6
libquadmath0 >= 4.6

Download

Type URL
Binary Package tm-align_20120507-1_i386.deb
Source Package tm-align

Install Howto

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

Files

Path
/usr/bin/TMalign
/usr/bin/TMscore
/usr/share/doc/tm-align/README.Debian
/usr/share/doc/tm-align/changelog.Debian.gz
/usr/share/doc/tm-align/copyright
/usr/share/man/man1/TMalign.1.gz
/usr/share/man/man1/TMscore.1.gz

Changelog

2012-06-29 - Andreas Tille <tille@debian.org>
tm-align (20120507-1) unstable; urgency=low
* New upstream version
* debian/rules: Add hardening options
2012-03-08 - Andreas Tille <tille@debian.org>
tm-align (20120124-1) unstable; urgency=low
[ Charles Plessy ]
* debian/upstream: renamed from upstream-metadata.yaml
[ Andreas Tille ]
* New upstream version
* debian/upstream:
- Fixed typo (s/TITILE/TITLE/)
- Moved DOI+PMID to references
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debhelper 9 (control+compat)
* debian/changelog: DEP5 verified using
cme fix dpkg-copyright
2011-10-21 - Andreas Tille <tille@debian.org>
tm-align (20111012-1) unstable; urgency=low
* New upstream release
* Enhances t-coffee
* Standards-Version: 3.9.2 (no changes needed)
* Debhelper 8 (control + compat)
* Fixed Vcs fields
2011-02-05 - Steffen Moeller <moeller@debian.org>
tm-align (20110130-2) unstable; urgency=low
* New upstream version (Closes: #447505)
- 2011/01/30: An open source license is attached to the program
* Reverting changelog to keep the history.
2011-01-30 - Andreas Tille <tille@debian.org>
tm-align (20110130-1) UNRELEASED; urgency=low
* Initial release.
2011-01-30 - Tim Booth <tbooth@ceh.ac.uk>
tm-align (20110124-1) UNRELEASED; urgency=low
* New upstream version
- 2005/06/01: A small bug of two-point superposition was fixed.
- 2005/10/19: the program was reformed so that the alignment results
are not dependent on the specific compilers.
- 2006/06/20: select 'A' if there is altLoc when reading PDB file.
- 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
- 2007/04/18: added options with TM-score normalized by average
length, shorter length, or longer length of two
structures.
- 2007/05/23: added additional output file 'TM.sup_all' for showing
all atoms while 'TM.sup' is only for aligned atoms
- 2007/09/19: added a new feature alignment to deal with the problem
of aligning fractional structures (e.g. protein
interfaces).
- 2007/10/16: A bug for irregular bond-length models was fixed.
- 2009/03/14: A new initial alignment was added and previous initial
alignments are further enhanced. This change increased
accuracy by 4% but increases CPU cost by 40%.
- 2009/08/20: A bug for asymmetry alignment result was fixed.
- 2010/08/02: A new RMSD matrix was used to remove obsolete
statements. Staled subroutines were deleted.
- 2011/01/03: The length of pdb file names were extended to 500
- 2011/01/24: Fixed a bug on output file name created on 2011/01/03 
* Tweaked get-orig-source in rules to spot version in upstream file
* New standards version 3.9.4
2008-02-06 - David Paleino <d.paleino@gmail.com>
tm-align (20050601-2) UNRELEASED; urgency=low
* Updated to Standards-Version 3.7.3 (no changes needed)
2007-10-21 - Steffen Moeller <moeller@debian.org>
tm-align (20050601-1) UNRELEASED; urgency=low
* Initial packaging.

See Also

Package Description
tmake_1.8-1.1_i386.deb a cross-platform makefile tool
tmexpand_0.1.2.0-3_all.deb text-macro processing script to create HTML and SGML documents
tmispell-voikko_0.7.1-3_i386.deb Ispell wrapper which uses Voikko for spell-checking
tmpreaper_1.6.13+nmu1_i386.deb cleans up files in directories based on their age
tmux_1.6-2_i386.deb terminal multiplexer
tmw-music_0.3-3_all.deb The Mana World is a 2D MMORPG (music files)
tmw_20110911-3_all.deb The Mana World is a 2D MMORPG
tnat64_0.05-1_i386.deb IPv4 to NAT64 redirector
tnef_1.4.9-1_i386.deb Tool to unpack MIME application/ms-tnef attachments
tnftp_20100108-3_i386.deb enhanced ftp client
tntdb-mysql3_1.2-2+b1_i386.deb MySQL backend for tntdb database access library
tntdb-postgresql3_1.2-2+b1_i386.deb PostgreSQL backend for tntdb database access library
tntdb-sqlite3_1.2-2+b1_i386.deb SQLite backend for tntdb database access library
tntnet-demos_2.1-2+deb7u1_i386.deb demo web applications for Tntnet
tntnet-doc_2.1-2+deb7u1_all.deb documentation for Tntnet
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