Nussinov’s algorithm

RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model.

10p viflorida2711 30-10-2020 19 2   Download

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov’s classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses.

16p viconnecticut2711 29-10-2020 6 1   Download

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology.

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An RNA primary structure, or sequence, is a single strand considered as a chain of nucleotides from the alphabet AUGC (adenine, uracil, guanine, cytosine). The strand can be folded onto itself, i.e., one segment of an RNA sequence might be paired with another segment of the same RNA sequence into a two-dimensional structure composed by a list of complementary base pairs, which are close together with the minimum energy.

11p vijisoo2711 27-10-2020 11 1   Download