Conserved secondary structure prediction for similar highly group of related RNA sequences

摘要：

Successfully predicting the conserved structure of a group of related RNAs plays an important role in identifying their functions. In this paper, we propose a new scheme to tackle this problem by using information of stem occurrence frequency. Our method was tested against ten groups of HIV-1 isolates and all ten predicted conserved secondary structures were perfectly consistent with the wild type structure. The method showed to be very efficient for similar highly RNA sequences. Besides, the time complexity of our algorithm is O(n2m2) where the group considered consists of m isolate RNA sequences and every sequence has roughly n-length nucleotide bases.

关键词： stem occurrence information HIV-1 RRE HIV-1 mother-infant vertical transmission

作者: Haoyue Fu Dingyu Xue Xiangde Zhang Cangzhi Jia

作者单位: College of Information Science and Engineering,Northeastern University,Shenyang,110004,China;College College of Information Science and Engineering,Northeastern University,Shenyang,110004,China College of Sciences,Northeastern University,Shenyang,110004,China

会议类型: 国际会议

会议名称: 2009年中国控制与决策会议(2009 Chinese Control and Decision Conference)

会议地点: 广西桂林

会议语种:英文

页码: 5158-5163

在线出版日期: 2009-06-17（万方平台首次上网日期，不代表论文的发表时间）