Liu Jingping, Ma Bin, Zhang Kaizhong
Department of Computer Science, University of Western Ontario, London, Ontario, Canada.
Biomol Eng. 2007 Sep;24(3):343-50. doi: 10.1016/j.bioeng.2007.02.005. Epub 2007 Mar 3.
RNA molecules, which are found in all living cells, fold into characteristic structures that account for their diverse functional activities. Many of these RNA structures consist of a collection of fundamental RNA motifs. The various combinations of RNA basic components form different RNA classes and define their unique structural and functional properties. The availability of many genome sequences makes it possible to search computationally for functional RNAs. Biological experiments indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop regions. The searching for those well-ordered RNA structures and their homologues in genomic sequences is very helpful for the understanding of RNA-based gene regulation. In this paper, we consider the following problem: given an RNA sequence with a known secondary structure, efficiently determine candidate segments in genomic sequences that can potentially form RNA secondary structures similar to the given RNA secondary structure. Our new bottom-up approach searches all potential stem-loops similar to ones of the given RNA secondary structure first, and then based on located stem-loops, detects potential homologous structural RNAs in genomic sequences.
RNA分子存在于所有活细胞中,会折叠成特定结构,这些结构决定了它们多样的功能活动。许多这类RNA结构由一系列基本的RNA基序组成。RNA基本成分的各种组合形成了不同的RNA类别,并定义了它们独特的结构和功能特性。众多基因组序列的可得性使得通过计算搜索功能RNA成为可能。生物学实验表明,功能RNA具有特征性的RNA结构基序,这些基序由环区特定的碱基配对组合和保守核苷酸所代表。在基因组序列中搜索那些有序的RNA结构及其同源物,对于理解基于RNA的基因调控非常有帮助。在本文中,我们考虑以下问题:给定一个具有已知二级结构的RNA序列,有效地确定基因组序列中可能形成与给定RNA二级结构相似的RNA二级结构的候选片段。我们新的自底向上方法首先搜索所有与给定RNA二级结构相似的潜在茎环,然后基于找到的茎环,在基因组序列中检测潜在的同源结构RNA。