Summary
TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller 0.2 indicates that there is no similarity between two structures; a TM-score greater 0.5 means the structures share the same fold. What is the difference between TM-score and TM-align? The TM-score program is to compare two models based on their given and known residue equivalency. It is usually NOT applied to compare two proteins of different sequences. The TM-align is a structural alignment program for comparing two proteins whose sequences can be different. The TM-align will first find the best equivalent residues of two proteins based on the structure similarity and then output a TM-score. The TM-score values in both programs have the same definition.
Versions
v20150914-r1 :: 0 :: gentoo
- Modified
- License
- tm-align
- Keywords
- amd64 ppc64 ~amd64-linux ~ppc ~x86 ~x86-linux
- USE flags
- custom-cflags
USE flags
General
- custom-cflags
- Build with user-specified CFLAGS (unsupported)
Dependencies
Runtime Dependencies
Depending packages
sci-biology / t-coffee : A multiple sequence alignment package
Change logs
- Repository mirror & CI · gentoo
Merge updates from master - Arthur Zamarin · gentoo
sci-chemistry/tm-align: destabilize for ~x86
Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/tm-align: Drop 20150914 (r0)
Closes: https://bugs.gentoo.org/834302 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Agostino Sarubbo · gentoo
sci-chemistry/tm-align: x86 stable wrt bug #834302
Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-chemistry/tm-align: ppc64 stable wrt bug #834302
Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --include-arches="ppc64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Agostino Sarubbo · gentoo
sci-chemistry/tm-align: amd64 stable wrt bug #834302
Package-Manager: Portage-3.0.30, Repoman-3.0.3 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Sam James · gentoo
sci-chemistry/tm-align: update EAPI 6 -> 8
Bug: https://bugs.gentoo.org/834302 Signed-off-by: Sam James <sam@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Georgy Yakovlev · gentoo
sci-chemistry/tm-align: de-stabilize for ~ppc, bug #823768
Bug: https://bugs.gentoo.org/823768 Signed-off-by: Georgy Yakovlev <gyakovlev@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/tm-align: Drop old
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11 - Repository mirror & CI · gentoo
Merge updates from master - Thomas Deutschmann · gentoo
sci-chemistry/tm-align: x86 stable (bug #668654)
Package-Manager: Portage-2.3.51, Repoman-2.3.11 Signed-off-by: Thomas Deutschmann <whissi@gentoo.org> - Repository mirror & CI · gentoo
Merge updates from master - Mikle Kolyada · gentoo
sci-chemistry/tm-align: amd64 stable wrt bug #668654
Signed-off-by: Mikle Kolyada <zlogene@gentoo.org> Package-Manager: Portage-2.3.49, Repoman-2.3.11 - Repository mirror & CI · gentoo
Merge updates from master - Sergei Trofimovich · gentoo
sci-chemistry/tm-align: stable 20150914 for ppc/ppc64, bug #668654
Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11 RepoMan-Options: --include-arches="ppc ppc64" - Repository mirror & CI · gentoo
Merge updates from master - Andreas Sturmlechner · gentoo
sci-chemistry/tm-align: EAPI-6 bump
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org> Package-Manager: Portage-2.3.51, Repoman-2.3.11 - David Seifert · gentoo
sci-chemistry/tm-align: [QA] Add cmake-utils_src_prepare
Package-Manager: Portage-2.3.11, Repoman-2.3.3 - Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> - Justin Lecher · gentoo
sci-chemistry/tm-align: Version Bump
Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org> - Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed