MultiSeq: unifying sequence and structure data for evolutionary analysis.
MultiSeq: unifying sequence and structure data for evolutionary analysis.
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Multiseq：统一的序列和结构数据以进行进化分析。
DOI：
10.1186/1471-2105-7-382
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发表时间：
2006-08-16
影响因子：
3
通讯作者：
Luthey-Schulten, Zaida
中科院分区：
文献类型：
--
作者：
Roberts, Elijah;Eargle, John;Wright, Dan;Luthey-Schulten, Zaida
自2000年人类基因组第一稿发表以来，生物信息学数据一直在以压倒性的速度积累。目前，公共数据库中有超过300万个蛋白质和核酸的序列和3.5万个结构。寻找这些数据之间的相关性来回答关键的研究问题是极其具有挑战性的。这个问题需要从几个方向来解决：组织和搜索数据的信息科学；帮助识别相关性的信息可视化；制定统计推论的数学；以及分析序列和结构变化方面的化学和物理性质的生物学。在这里，我们介绍了MultiSeq，一个统一的生物信息学分析环境，允许人们组织、显示、比对和分析蛋白质和核酸的序列和结构数据。虽然特别强调在进化生物学的框架内分析数据，但环境也足够灵活，可以适应其他使用模式。进化方法通过使用预定义的元数据、遵守标准的本体论映射以及用户使用电子笔记本调整这些分类的能力来支持。MultiSeq包含一种新的算法，可以生成完整的进化概况，代表一组同源的远亲蛋白质的分子系统发生树的拓扑结构。该方法基于多个序列和结构比对的多维QR因式分解，从比对中去除冗余，并通过增加线性相关性来对蛋白质序列进行排序，从而识别跨越同源蛋白质组进化空间的最小序列基集。MultiSeq是作为VMD的一部分提供的多重比对工具的主要扩展，VMD是用于分析分子动力学模拟的结构可视化程序。两者都是由美国国立卫生研究院高分子建模和生物信息学资源免费分发的，从1.8.5版开始，MULTERSEQ包括在VMD中。MultiSeq网站提供了有关如何下载和使用该软件的详细信息：
Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software:
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DOI：
10.1002/prot.340230412
发表时间：
1995-12-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Frishman, D;Argos, P
通讯作者：
Argos, P
影响因子：
3.4
作者：
BERMAN, HM;OLSON, WK;SCHNEIDER, B
通讯作者：
SCHNEIDER, B
影响因子：
1.3
作者：
Eastwood, MP;Hardin, C;Wolynes, PG
通讯作者：
Wolynes, PG
EMBL核苷酸序列数据库：2005年的发展。
影响因子：
14.9
作者：
Cochrane, Guy;Aldebert, Philippe;Althorpe, Nicola;Andersson, Mikael;Baker, Wendy;Baldwin, Alastair;Bates, Kirsty;Bhattacharyya, Sumit;Browne, Paul;van den Broek, Alexandra;Castro, Matias;Duggan, Karyn;Eberhardt, Ruth;Faruque, Nadeem;Gamble, John;Kanz, Carola;Kulikova, Tamara;Lee, Charles;Leinonen, Rasko;Lin, Quan;Lombard, Vincent;Lopez, Rodrigo;McHale, Michelle;McWilliam, Hamish;Mukherjee, Gaurab;Nardone, Francesco;Pastor, Maria Pilar Garcia;Sobhany, Siamak;Stoehr, Peter;Tzouvara, Katerina;Vaughan, Robert;Wu, Dan;Zhu, Weimin;Apweiler, Rolf
通讯作者：
Apweiler, Rolf
影响因子：
14.9
作者：
Andreeva, A;Howorth, D;Murzin, AG
通讯作者：
Murzin, AG