MSAT: a multiple sequence alignment tool based on TOPS.
MSAT: a multiple sequence alignment tool based on TOPS.
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DOI：
10.2165/00822942-200403020-00009
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发表时间：
2004-01-01
期刊：
影响因子：
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通讯作者：
Gilbert, David
中科院分区：
文献类型：
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作者：
Ren, Te;Veeramalai, Mallika;Gilbert, David
本文介绍了一种基于折叠水平蛋白质结构比对的多序列比对新方法的开发，与最常用的仅基于序列的技术相比，该方法提高了准确性。该方法将广泛使用的渐进式多序列比对方法 ClustalW 与基于蛋白质结构拓扑 (TOPS) 拓扑的比对算法相结合。 TOPS 方法通过使用基于拓扑的模式发现程序对输入蛋白质集进行结构比对，提供一组匹配的序列区域，可用于使用 ClustalW 指导序列比对。所得到的比对比仅序列比对更可靠，这是通过使用 CATH 数据库中分布在七个超折叠家族的一组 106 个蛋白质示例进行 20 倍交叉验证确定的。该方法对于在折叠水平上具有相似结构但序列同一性较低的蛋白质组特别有效。这项研究的目的是为弥合蛋白质序列和结构分析之间的差距做出贡献，希望能够帮助理解序列、结构和功能之间的关系。该工具可从 http://balabio.dcs.gla.ac.uk/msat/ 获取。
This article describes the development of a new method for multiple sequence alignment based on fold-level protein structure alignments, which provides an improvement in accuracy compared with the most commonly used sequence-only-based techniques. This method integrates the widely used, progressive multiple sequence alignment approach ClustalW with the Topology of Protein Structure (TOPS) topology-based alignment algorithm. The TOPS approach produces a structural alignment for the input protein set by using a topology-based pattern discovery program, providing a set of matched sequence regions that can be used to guide a sequence alignment using ClustalW. The resulting alignments are more reliable than a sequence-only alignment, as determined by 20-fold cross-validation with a set of 106 protein examples from the CATH database, distributed in seven superfold families. The method is particularly effective for sets of proteins that have similar structures at the fold level but low sequence identity. The aim of this research is to contribute towards bridging the gap between protein sequence and structure analysis, in the hope that this can be used to assist the understanding of the relationship between sequence, structure and function. The tool is available at http://balabio.dcs.gla.ac.uk/msat/.