A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction

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http://doi.ieeecomputersociety.org/10.1109/ICPP.2006.10

2006 International Conference on Para ...

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	ASCII Text	x
	Wenduo Zhou, David K. Lowenthal, "A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction," Parallel Processing, International Conference on, pp. 74-81, 2006 International Conference on Parallel Processing (ICPP'06), 2006.

	BibTex	x
	@article{ 10.1109/ICPP.2006.10, author = {Wenduo Zhou and David K. Lowenthal}, title = {A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction}, journal ={Parallel Processing, International Conference on}, volume = {0}, year = {2006}, issn = {0190-3918}, pages = {74-81}, doi = {http://doi.ieeecomputersociety.org/10.1109/ICPP.2006.10}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - Parallel Processing, International Conference on TI - A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction SN - 0190-3918 SP74 EP81 A1 - Wenduo Zhou, A1 - David K. Lowenthal, PY - 2006 KW - null VL - 0 JA - Parallel Processing, International Conference on ER -

Wenduo Zhou, University of Georgia, USA

David K. Lowenthal, University of Georgia, USA

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, distributedmemory 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.

Citation:

Wenduo Zhou, David K. Lowenthal, "A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction," icpp, pp.74-81, 2006 International Conference on Parallel Processing (ICPP'06), 2006

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