A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows

Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2012

Volumn , Issue , 2012, Pages 86-93

  Zhang, Boyu ^a   Yehdego, Daniel T ^b   Johnson, Kyle L ^b   Leung, Ming Ying ^b   Taufer, Michela ^a  

^a University of Delaware   (United States)

^b UNIVERSITY OF TEXAS AT EL PASO   (United States)

Author keywords

bioinformatics; Hadoop; Parallel programming

Indexed keywords

HADOOP; MAPREDUCE FRAMEWORKS; PREDICTING SECONDARY STRUCTURE; PREDICTING THE SECONDARY STRUCTURES; RECONSTRUCTION PROCESS; RNA SECONDARY STRUCTURE PREDICTION; SECONDARY STRUCTURES; THERMODYNAMIC METHODS;

BIOINFORMATICS; GENE EXPRESSION; PARALLEL PROGRAMMING; RNA;

FORECASTING;

EID: 84875588947     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2012.6470251     Document Type: Conference Paper

References (17)

1. M. Taufer, et al., "RNAVLab: A virtual laboratory for studying rna secondary structures based on grid computing technology," J. Par. Computing, 34(11):661-680, 2008.
2. E. Rivas and S. Eddy,''A dynamic programming algorithm for RNA structure prediction including pseudoknots," J. Mol. tu, 285: 2053-2068,1999.
3. M. Taufer, et al., "On the effectiveness of rebuilding RNA secondary structures from sequence chunks," in Proc. of the 7th IEEE International Workshop on High Performance Computational Biology, April 2008.
4. J. Dean and S. Ghemawat, "MapReduce: Simplified data processing on large clusters," in Proc. of the 6th Symposium on Opearting Systems Design and Implementation, December 2004.
5. ''Apache hadoop," http://hadoop. apache. org/.
6. A. Licon, et al., ''A dynamic programming algorithm for finding the optimal segmentation of an RNA secondary structure prediction," in Proc. of the International Conference on Bioinformatics and Computational Biology, March 2010.
7. D. Hong, et al., "Fx: an RNA-seq analysis tool on the cloud," Bioinformaiics, 28(5):721-723, 2012.
8. Evaluation of a practical pseudoknot folding algorithm based on thermodynamics," BMC Bioinform, 5:104, 2004.
9. B. Langmead, et al., "Cloud-scale RNA-sequencing differential expression analysis with myrna," Genome Biology, 11:R83, 2011.
10. D. Thain, et al., "Distributed computing in practice: the condor experience," J. Concurrency and Computation: Practice and Experience, 17(2-4):323-356, 2005.
11. D. Yehdego.et al., "Poster: Secondary structure predictions for long RNA sequences based on inversion excursions," in Proc. of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, October 2012.
12. J. Reeder and R. Giegerich, "Design, implementation, and evaluation of a practical pseudoknot folding algorithm based on thermodynamics," BMC Bioinform, 5:104, 2004.
13. I.L. Hofacker, et al., "Fast folding and comparison of RNA secondary structures," Monatshefte f. Chemie 125: 167-18, 1994.
14. N.R. Markham and M. Zuker, "UNAFold: Software for nucleic acid folding and hybridization in data, dequence analysis, and evolution," Bioinformatics 2(1): 3-31, 2008.
15. C. Aksay, et al., "TaveRNA: a web suite for RNA algorithms and applications," Nucleic Acids tu. 35:W325-W329, 2007.
16. J. Ren, et al., "HotKnots: heuristic prediction of RNA secondary structures including pseudoknots," RNA, 11, 14941504, 2005.
17. S. Griffiths-Jones, et al., "Rfam: annotating non-coding RNAs in complete genomes," Nucleic Acids Research 33(suppl1):D121-D124, 2005.