3DCoffee@igs：一个用于将序列和结构合并为多序列比对的网络服务器。
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.
作者信息
Poirot Olivier, Suhre Karsten, Abergel Chantal, O'Toole Eamonn, Notredame Cedric
机构信息
Information Génomique et Structurale UPR2589-CNRS, CNRS, 31, Chemin Joseph Aiguier, 13 402 Marseille Cedex 20, France.
出版信息
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. doi: 10.1093/nar/gkh382.
Abstract
This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.
摘要
本文介绍了3DCoffee@igs，这是一个基于网络的工具，专门用于高质量多序列比对（MSA）的计算。3D-Coffee能够混合蛋白质序列和结构，以提高比对的准确性。结构既可以作为PDB标识符提供，也可以直接上传到服务器。给定一组序列和结构，结构对使用SAP进行比对，而序列-结构对则使用Fugue进行比对。然后，将所得的成对比对集合通过T-Coffee算法组合成一个MSA。该服务器及其文档可从http://igs-server.cnrs-mrs.fr/Tcoffee/获取。
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本文引用的文献
1
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
Bioinformatics. 2003;19 Suppl 1:i215-21. doi: 10.1093/bioinformatics/btg1029.
2
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.
Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. doi: 10.1093/nar/gkg522.
3
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
Nucleic Acids Res. 2003 Jul 1;31(13):3320-3. doi: 10.1093/nar/gkg556.
4
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Res. 2003 Jan 1;31(1):315-8. doi: 10.1093/nar/gkg046.
5
Human non-synonymous SNPs: server and survey.
Nucleic Acids Res. 2002 Sep 1;30(17):3894-900. doi: 10.1093/nar/gkf493.
6
Accounting for human polymorphisms predicted to affect protein function.
Genome Res. 2002 Mar;12(3):436-46. doi: 10.1101/gr.212802.
7
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.
Bioinformatics. 2001 Aug;17(8):748-9. doi: 10.1093/bioinformatics/17.8.748.
8
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
J Mol Biol. 2001 Jun 29;310(1):243-57. doi: 10.1006/jmbi.2001.4762.
9
Multiple sequence alignment in phylogenetic analysis.
Mol Phylogenet Evol. 2000 Sep;16(3):317-30. doi: 10.1006/mpev.2000.0785.
10
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042.
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