Novel Algorithms for NcRNA Discovery and RNA Structure Prediction

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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.