RNAMotif, an RNA secondary structure definition and search algorithm
RNAMotif, an RNA secondary structure definition and search algorithm
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DOI：
10.1093/nar/29.22.4724
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发表时间：
2001-11-15
影响因子：
14.9
通讯作者：
Sampath, R
中科院分区：
文献类型：
--
作者：
Macke, TJ;Ecker, DJ;Sampath, R
RNA分子折叠成特征二级和第三级结构，这些结构解释了它们的各种功能活性。这些RNA结构中的许多是从RNA结构基序集合中组装的。这些基本的构建块反复使用，并以各种组合形成不同的RNA类型并定义其独特的结构和功能特性。因此，重复出现的RNA结构基序的鉴定将增强我们对RNA结构的理解，并帮助RNA结构与功能和调节元件的关联。我们的目标是开发一个计算机程序，该程序可以描述任何复杂性的RNA结构元素，然后搜索这些结构元素的任何核苷酸序列数据库，包括完整的原核和真核基因组。在这里，我们详细描述了一种新的计算图案搜索算法，rnamotif，并通过一些主题搜索示例演示了其实用性。 rnamotif在两个重要方面与其他主题搜索工具有所不同：第一，结构定义语言更灵活，可以指定任何类型的基本基础交互；其次，rnamotif提供了一个用户控制的评分部分，该部分可用于添加单独使用模式无法提供的功能。
RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.