Multiple RNA Interaction: Beyond Two

PROJECT TITLE :

Multiple RNA Interaction: Beyond Two

ABSTRACT:

The interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. But, biological mechanisms in that more than two RNAs take part in an interaction also exist. It's cheap to believe that interactions involving multiple RNAs are usually a lot of complex to be treated pairwise. In addition, given a pool of RNAs, it is not trivial to predict that RNAs interact without sufficient biological knowledge. Therefore, structures resulting from multiple RNA interactions typically cannot be predicted by the present algorithms that handle RNAs pairwise and may simply favor the simplest interacting try. We tend to propose a system for multiple RNA interaction that overcomes the difficulties mentioned on top of by formulating a combinatorial optimization drawback known as Pegs and Rubber Bands. A answer to this drawback encodes a structure of interacting RNAs. The matter, not surprisingly, is NP-onerous. But, our experiments with approximation algorithms and heuristics for the matter counsel that this formulation is adequate to predict known interaction patterns of multiple RNAs. Generally, however, the optimal answer obtained does not essentially correspond to the particular structure observed in biological experiments. Moreover, a structure made by interacting RNAs may not be unique. We tend to extend our approach to come up with multiple suboptimal solutions. By clustering these solutions, we tend to will be able to reveal representatives that correspond to realistic structures. Specifically, our results on the U2-U6 advanced with introns in the spliceosome of human/yeast and the CopA-CopT complicated in E. coli are according to revealed biological structures.

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