Tuning iteration space slicing based tiled multi-core code implementing Nussinov’s RNA folding

Tuning iteration space slicing based tiled multi-core code implementing Nussinov’s RNA folding

Abstract Background 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. Fortunately, RNA secondary structure approaches, such as Nussinov’s recurrence,...

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Bibliographic Details
Main Authors: Marek Palkowski, Wlodzimierz Bielecki
Format: Article
Language:English
Published: BMC 2018-01-01
Series:BMC Bioinformatics
Subjects:
RNA folding
Parametric loop tiling
Computational biology
Nussinov’s algorithm
Parallel computing
Tile size selection
Online Access:http://link.springer.com/article/10.1186/s12859-018-2008-6

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http://link.springer.com/article/10.1186/s12859-018-2008-6

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