Tiling Nussinov’s RNA folding loop nest with a space-time approach

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 208 - 11
• Main Authors: Palkowski, Marek, Bielecki, Wlodzimierz
• Format: Journal Article
• Language: English
• Published: London BioMed Central 24.04.2019; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Adenine; Algorithms; Amino acid sequence; Analysis; Base pairs; Bioinformatics; Biomedical and Life Sciences; Compilers; Computational biology; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Cytosine; Decomposition; Dependence; Dynamic programming; Folding; Guanine; International conferences; Life Sciences; Loop tiling; Methods; Microarrays; Nucleotide sequence; Nucleotides; Nussinov’s algorithm; Optimization theory; Parallel computing; Predictions; Protein structure; Purines; Pyrimidines; Research Article; Ribonucleic acid; RNA; RNA folding; RNA sequencing; Secondary structure; Space-time tiling; Spacetime; Structural analysis; Tiling; Time; Uracil; Values; Workshops; Poland; RNA folding; Space-time tiling; Parallel computing; Nussinov’s algorithm; Loop tiling
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2785-6

Background 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. That list is called RNA’s secondary structure and is predicted by an RNA folding algorithm. RNA secondary structure prediction is a computing-intensive task that lies at the core of search applications in bioinformatics. Results We suggest a space-time tiling approach and apply it to generate parallel cache effective tiled code for RNA folding using Nussinov’s algorithm. Conclusions Parallel tiled code generated with a suggested space-time loop tiling approach outperforms known related codes generated automatically by means of optimizing compilers and codes produced manually. The presented approach enables us to tile all the three loops of Nussinov’s recurrence that is not possible with commonly known tiling techniques. Generated parallel tiled code is scalable regarding to the number of parallel threads – increasing the number of threads reduces code execution time. Defining speed up as the ratio of the time taken to run the original serial program on one thread to the time taken to run the tiled program on P threads, we achieve super-linear speed up (a value of speed up is greater than the number of threads used) for parallel tiled code against the original serial code up to 32 threads and super-linear speed up scalability (increasing speed up with increasing the thread number) up to 8 threads. For one thread used, speed up is about 4.2 achieved on an Intel Xeon machine used for carrying out experiments.