TY - GEN
T1 - A parallel, out-of-core algorithm for RNA secondary structure prediction
AU - Zhou, Wenduo
AU - Lowenthal, David K.
PY - 2006
Y1 - 2006
N2 - RNA pseudoknot prediction is an algorithm for RNA sequence search and alignment. An important building block towards pseudoknot prediction is RNA secondary structure prediction. The difficulty of extending the secondary structure prediction algorithm to a parallel program is (1) it has complicated data dependences, and (2) it has a large data set that typically cannot fit completely in main memory. In this paper, we propose a new out-of-core, distributed-memory algorithm for RNA secondary structure prediction. Its novelty lies in its redundant file scheme, I/O-reducing in-core buffer mechanism, and dynamic load balancing algorithm. Experimental results obtained on 16 Sun UltraSPARC IIIi nodes provide evidence that our approach achieves good speedup. Furthermore, we found that counterintuitively, the size of the in-memory buffer is critical to efficiency of the parallel program.
AB - RNA pseudoknot prediction is an algorithm for RNA sequence search and alignment. An important building block towards pseudoknot prediction is RNA secondary structure prediction. The difficulty of extending the secondary structure prediction algorithm to a parallel program is (1) it has complicated data dependences, and (2) it has a large data set that typically cannot fit completely in main memory. In this paper, we propose a new out-of-core, distributed-memory algorithm for RNA secondary structure prediction. Its novelty lies in its redundant file scheme, I/O-reducing in-core buffer mechanism, and dynamic load balancing algorithm. Experimental results obtained on 16 Sun UltraSPARC IIIi nodes provide evidence that our approach achieves good speedup. Furthermore, we found that counterintuitively, the size of the in-memory buffer is critical to efficiency of the parallel program.
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U2 - 10.1109/ICPP.2006.10
DO - 10.1109/ICPP.2006.10
M3 - Conference contribution
AN - SCOPUS:34547423242
SN - 0769526365
SN - 9780769526362
T3 - Proceedings of the International Conference on Parallel Processing
SP - 74
EP - 81
BT - ICPP 2006
T2 - ICPP 2006: 2006 International Conference on Parallel Processing
Y2 - 14 August 2006 through 18 August 2006
ER -