Load balancing algorithm in cluster-based RNA secondary structure prediction

ISPDC 2005: 4th International Symposium on Parallel and Distributed Computing

Volumn 2005, Issue , 2005, Pages 91-96

  Guangming, Tan ^a,b   Shengzhong, Feng ^a   Ninghui, Sun ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTER SYSTEMS; COMPUTATIONAL BIOLOGY; DYNAMIC MAPPING; SECONDARY STRUCTURE;

DYNAMIC PROGRAMMING; MAPPING; PARALLEL ALGORITHMS; PROGRAM PROCESSORS; RESOURCE ALLOCATION; RNA;

COMPUTATIONAL METHODS;

EID: 33847727070     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISPDC.2005.32     Document Type: Conference Paper

References (14)

1. E Rivas and S Eddy. A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of Molecular Biology. Vol.285, pp:2053-2068. 1999
2. S Eddy and R Durbin. RNA sequence analysis using covariance models. Nuclear Aicds Research. Vol.22(11), pp;2079-2088. 1994.
3. S Eddy. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics, Vol.3:18, 2002
4. Y Sakakibara, M Brown. Stochastic context-free grammar for tRNA modeling. Nuclear Aicds Research. Vol. 22(23), pp:5112-5120, 1994
5. K. Lari and S Young. The estimation of stochastic context-free grammars using the inside-outside algorithm. Computer. Speech Language. Vol.4, pp:35-36, 1990
6. E.W Myers and W Miller. Optimal alignments in linear space. Computer Applications in the Bioscience Vol.4, pp:11-17, 1988
7. M.S Waterman and M Eggert. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. Journal of Molecular Biology. Vol. 197, pp:723-728, 1987
8. L.J.Guibas, H.T.Kung, C.D. Thompson. Direct VLSI Implementation of combination algorithms. In proceedings of Conference on Very Large Scale Integration. California Institute of Technology, pp:509-525, 1979
9. Kumiko Wada and Nobuyuki Ichiyoshi. A distributed shortest path algorithm and its mapping on the multi-PSI. In Proceedings of Distributed Massively Concurent Computers, 1989
10. Kai Hwang and Zhiwei Xu. Scalable Parallel Computing: Technology, Architecture, Programming. McGraw-Hill.1999
11. A Grama, A Gupta, G Karypis, V Kumar. Introduction to Parallel Computing. Addison Wesley, 2003
12. Parallel Dynamic Programming. PhD dissertation by Phillip Gnassi Bradford, 1994
13. Aluru, S., Fuamura, N., Mehrotra, K. Parallel Biological Sequence Comparison using Prefix Computation, Journal of Parallel and Distributed Computing, Vol.63, pp:264-272 ,2003
14. Brown, M.P. Small Subunit Ribosomal RNA Modeling using Stochastic Context-Free Grammars, Proceedings ISMB00, pp:57-66, 2000