A parallel, out-of-core algorithm for RNA secondary structure prediction

Wenduo Zhou, David K. Lowenthal

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Scopus citations

Abstract

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.

Original languageEnglish (US)
Title of host publicationICPP 2006
Subtitle of host publicationProceedings of the 2006 International Conference on Parallel Processing
Pages74-81
Number of pages8
DOIs
StatePublished - Dec 1 2006
Externally publishedYes
EventICPP 2006: 2006 International Conference on Parallel Processing - Columbus, OH, United States
Duration: Aug 14 2006Aug 18 2006

Publication series

NameProceedings of the International Conference on Parallel Processing
ISSN (Print)0190-3918

Other

OtherICPP 2006: 2006 International Conference on Parallel Processing
CountryUnited States
CityColumbus, OH
Period8/14/068/18/06

ASJC Scopus subject areas

  • Hardware and Architecture
  • Engineering(all)

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