Exploring microbial genome sequences to identify protein families on the grid

IEEE Transactions on Information Technology in Biomedicine

Volumn 11, Issue 4, 2007, Pages 435-442

  Sun, Yudong ^a,b   Wipat, Anil ^a   Pocock, Matthew ^a   Lee, Peter A ^a   Flanagan, Keith ^a   Worthington, James T ^a,c  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c Newcastle University ^*  (United Kingdom)

Author keywords

Genome analysis; Grid; Microbial genomes; Protein families; Web services

Indexed keywords

GENOME ANALYSIS; GENOME SEQUENCES; MICROBIAL GENOMES; POTENTIAL THERAPEUTIC TARGETS;

ANTIBIOTICS; PROTEINS; WEB SERVICES;

GENES;

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; CHROMOSOME MAP; CLASSIFICATION; GENETICS; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; MULTIGENE FAMILY; PROTEIN DATABASE;

BACTERIAL PROTEINS; CHROMOSOME MAPPING; DATABASES, PROTEIN; GENOME, BACTERIAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MULTIGENE FAMILY;

EID: 34547130575     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2007.892913     Document Type: Article

References (16)

1. M. T. Black and J. Hodgson, "Novel target sites in bacteria for overcoming antibiotic resistance" Adv. Drug Del. Rev., vol. 57, no. 10, pp. 1528-1538, 2005.
2. H. Loferer, "Mining bacterial genomes for antimicrobial targets," Mol. Med. Today, vol. 6, pp. 470-474, 2000.
3. J. Rosamond and A. Allsop, "Harnessing the power of the genome in the search for new antibiotics," Science, vol. 287, no. 5460, pp. 1973-1976, 2000.
4. I. Foster and S. Tuecke, "Describing the elephant: The different faces of IT as service," ACM Queue, vol. 3, no. 6, pp. 26-29, 2005.
5. I. Foster, C. Kesselman, J. M. Nick, and S. Tuecke, "Grid services for distributed system integration," Computer, vol. 35, no. 6, pp. 37-46, 2002.
6. N. Jacq, C. Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata et al., "Grid as a bioinformatic tool," Parallel Comput., vol. 30, no. 9-10, pp. 999-1167, 2004.
7. M. Cornell, I. Alam,D. Soanes, H.Wong, M. Rattray, S.Hubbard et al. "e-Fungi: An e-science infrastructure for comparative functional genomics in fungal species," presented at the 4th U.K. e-Sci. All Hands Meet. (AHM 2005), Nottingham, U.K.
8. D. Sulakhe, A. Rodriguez, M. D. Souza, M. Wilde, V. Nefedova, I. Foster, and N. Maltsev, "GNARE: An environment for grid-based high-throughput genome analysis," in Proc. 5th IEEE Int. Symp. Cluster Comput. Grid (CCGrid 2005), Cardiff, U.K., May, pp. 455-462.
9. N. Maltsev, E. Glass, D. Sulakhe, A. Rodriguez, M. H. Syed, T. Bompada et al., "PUMA2-grid-based high-throughput analysis of genomes and metabolic pathways," Nucl. Acids Res., vol. 34, no. 1, pp. D369-D372, 2006.
10. R. L. Tatusov, M. Y. Galperin, D. A. Natale, and E. V. Koonin, "The COG database: A tool for genome-scale analysis of protein functions and evolution," Nucl. Acids Res., vol. 28, no. 1, pp. 33-36, 2000.
11. R. R. Chaudhuri, A. M. Khan, and M. J. Pallen, "coliBASE: An online database for Escherichia coli, Shigella and Salmonella comparative genomics," Nucl. Acids Res., vol. 32, pp. D296-D299, 2004.
12. R. Stevens, A. Robinson, and C. Goble, "myGrid: Personalised bioinformatics on the information grid," Bioinformatics, vol. 19, no. 1, pp. i302-i304, 2003.
13. R. Stevens, R. McEntire, C. A. Goble, M. Greenwood, J. Zhao, A. Wipat et al., "myGrid and the drug discovery process," Drug Discovery Today: BIOSILICO, vol. 2, no. 4, pp. 140-148, 2004.
14. A. Krishna, V. Tan, R. Lawley, S. Miles, and L. Moreau, "myGrid notification service," in Proc. U.K. e-Sci. All Hands Meet., Nottingham, U.K., 2003, pp. 475-482.
15. R. L. Tatusov, E. V. Koonin, and D. J. Lipman, "A genomic perspective on protein families," Science, vol. 278, pp. 631-637, 1997.
16. A. K. Bansal and T. E. Meyer, "Evolutionary analysis by whole-genome comparisons," J. Bacteriol., vol. 184, no. 8, pp. 2260-2272, 2002.