Novel Algorithms for NcRNA Discovery and RNA Structure Prediction

加州大学圣地亚哥分校获得了一项拨款，用于开发发现非编码RNA的新算法。非编码RNA正在迅速恢复其作为感兴趣分子的重要性。除了少数例外，大多数ncRNA都是通过实验发现的，发现ncRNA的有效、通用的计算工具仍然是一个未得到满足的需求。这一奖项侧重于比较方法，典型的问题如下：给定一个查询ncRNA序列和一个序列数据库，在数据库中找到在序列和二级结构上与查询匹配的所有序列。该提案的一个新颖部分是开发计算过滤器，这种过滤器可以快速消除大部分数据库，同时保留真正的同源基因，以便使用更昂贵的函数进行评估。与用于DNA/蛋白质数据库搜索的BLAST类似，基于过滤器的比较ncRNA搜索具有极大地加速发现新ncRNA的潜力。这项提议是对RNA过滤器的第一次系统研究。同样，在RNA的背景下，构建受保守种子结构限制的比对的想法是新颖的，并产生了令人兴奋的初步结果。提案中开发的工具将免费用于所有学术、研究和非商业目的，并应对更大的社区产生影响。这里开发的工具将是课程不可分割的一部分，并允许学生探索其他功能的RNA。

University of California - San Diego is awarded a grant to develop novel algorithms for discovering non-coding RNAs. Non-coding RNAs are rapidly regaining importance as a molecule of interest. Most ncRNA, with few exceptions, have been discovered through experiments, and effective, general computational tools for ncRNA discovery remain an unmet need. This award focuses on a comparative approach, typified by the following problem: given a query ncRNA sequence, and a sequence database, find all sequences in the database that match the query in sequence and secondary structure. A novel part of the proposal is the development of computational filters that rapidly eliminate much of the database, while retaining the true homologs to be evaluated using more expensive functions. Similar to BLAST for DNA/protein database search, filter based comparative ncRNA search has the potential to greatly accelerate discovery of novel ncRNA. This proposal is the first systematic study of RNA filters. Likewise, the idea of constructing alignments constrained by conserved seed structures is novel in the context of RNA and has yielded exciting preliminary results. The tools that are developed in the proposal will be free for all academic, research, and non-commercial purposes, and should have an impact on the larger community. The tools developed here will be an integral part of the curriculum, and allow students to explore other functional RNA.