Optimizing sequence alignment in cloud using hadoop and MPP database

Proceedings - 2012 IEEE 5th International Conference on Cloud Computing, CLOUD 2012

Volumn , Issue , 2012, Pages 819-827

  Vijayakumar, Senthilkumar ^a   Bhargavi, Anjani ^a   Praseeda, Uma ^a   Ahamed, Syed Azar ^a  

^a TATA CONSULTANCY SERVICES   (India)

Author keywords

Cloud Computing; Computational Biology; FASTA; Greenplum MPP Database; Hadoop; Sequence Alignment

Indexed keywords

BIOLOGICAL RESEARCH; COMPLEX NATURE; COMPUTATIONAL BIOLOGY; COMPUTING TECHNOLOGY; DATA SETS; EVOLUTIONARY RELATIONSHIPS; FASTA; HADOOP; LARGE DATASETS; MASSIVELY PARALLEL PROCESSING; MEDICAL RESEARCH; PARALLEL TECHNOLOGY; PETABYTES; SCIENTIFIC ANALYSIS; SEQUENCE ALIGNMENTS; SMITH-WATERMAN; STATE-OF-THE-ART TECHNOLOGY;

ALGORITHMS; ALIGNMENT; BIOINFORMATICS; CLOUD COMPUTING; DATABASE SYSTEMS; FIRE FIGHTING EQUIPMENT; HEURISTIC METHODS; OPTIMIZATION; PROTEINS; RNA;

DNA SEQUENCES;

EID: 84866745831     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CLOUD.2012.34     Document Type: Conference Paper

References (27)

1. GenBank Web Page. http://www.ncbi.nlm.nih.gov/genbank/
2. K. Asanovic, et al. The Landscape of Parallel Computing Research: A View from Berkeley. Technical Report EECS Department, University of California, Berkeley, Dec 2006.
3. F. Waas. "Beyond Conventional Data Warehousing - Massively Parallel Data Processing with Greenplum Database" In Proc. BIRTE, 2008.
4. Apache, Hadoop Documentation (2002), Available at http://hadoop.apache. org/core/docs/r0.17.2/.
5. David J. DeWitt2 Jim Gray "Parallel Database Systems: The Future of High Performance Database Processing" , Proc.Communications of the ACM, Vol. 36, No. 6, June 1992
6. OpenStack Web Page. http://openstack.org/
7. T. White, Hadoop - The Definitive Guide, Ed O'Reilly, June 2009.
8. Greenplum Web Page www.greenplum.com/community/
9. J.-C. Freytag. "A Rule-Based View of Query Optimization", In Proc. ACM-SIGMOD, pages 173-180, 1987.
10. WILLIAM R. PEARSON* AND DAVID J. LIPMAN, "Improved tools for biological sequence comparison", Proc. Natl. Acad. Sci. USA Vol. 85, pp. 2444-2448, April 1988, Biochemistry.
11. http://www.cs.sunysb.edu/~skiena/648/presentations/blast/FASTA.html
12. OpenStack Project. Multiple-Compute-Nodes Setup. Web Page.http://docs. openstack.org/trunk/openstackcompute/admin/content/configuring-multiple-compute- nodes.html
13. Ronald Taylor, Pacific Northwest National Laboratory, Richland, WA, "An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics", Bioinformatics Open Source Conference 2010
14. Gabriel Antoniu, Luc Bougé, INRIA Rennes, Bertrand Thirion, Jean- Baptiste Poline,INRIA France, "AzureBrain: Large-scale Joint Genetic and Neuroimaging Data Analysis on Azure Clouds", September 30, 2010
15. S. Fushimi, M. Kitsuregawa, and H. Tanaka "An Overview of the System Software of A Parallel Relational Database Machine" In VLDB '86, 1986.
16. R. Chaiken, B. Jenkins, P.-A. Larson, B. Ramsey, D. Shakib, S. Weaver, and J. Zhou "Scope: Easy and efficient parallel processing of massive data sets" In Proc. of VLDB, 2008.
17. http://bioinformatics.oxfordjournals.org/content/25/12/1475.full
18. Demonstration of FASTA at EBI, http://www.ebi.ac.uk/fasta/
19. http://compbio.pbworks.com/w/page/16252890/ Fast%20Sequence%20Similarity%20Search%20Algorithms
20. Introduction to bioinformatics, Autumn 2007, "Chapter 7: Rapid alignment methods: FASTA and BLAST", http://www.cs.helsinki.fi/ bioinformatiikka/mbi/courses/07-08/itb/slides/itb0708-slides-83-116.pdf
21. G. Sudha Sadasivam, G. Baktavatchalam, "A novel approach to multiple sequence alignment using hadoop data grids", Proc. MDAC '10 Proceedings of the 2010 Workshop on Massive Data Analytics on the Cloud, ACM New York, NY, USA ©2010
22. Azza Abouzeid, Kamil BajdaPawlikowski,Daniel Abadi, Avi Silberschatz, Alexander Rasin "HadoopDB: An Architectural Hybrid of MapReduce and DBMS Technologies for Analytical Workloads", VLDB '09, August 2428, 2009, Lyon, France.
23. A. Guazzelli, K. Stathatos, M. Zeller (2009). "Efficient Deployment of Predictive Analytics through Open Standards and Cloud Computing", The ACM SIGKDD Explorations Newsletter, Volume 11/1, July 2009.
24. Stein L. The case for cloud computing in genome informatics. Genome Biology.2010;11:207.doi: 10.1186/gb-2010-11-5-207. [PMC free article] [PubMed] [Cross Ref]
25. Michael C. Schatz, Center for Bioinformatics and Computational Biology, University of Maryland, "CloudBurst: highly sensitive read mapping with MapReduce", BIOINFORMATICS Vol. 25 no. 11 2009, pages 1363-1369 doi:10.1093/bioinformatics/btp236
26. Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly, Mark A. DePristo, "The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data", Published in Advance July 19, 2010, doi: 10.1101/gr.107524.110
27. Genome Res. 2010. 20: 1297-1303