MotifNetwork: A grid-enabled workflow for high-throughput domain analysis of biological sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 620-627

  Tilson, Jeffrey L ^a   Rendon, Gloria ^a   Ger, Mao Feng ^a   Jakobsson, Eric ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; BIOINFORMATICS; DATA VISUALIZATION; FLOW INTERACTIONS; KNOWLEDGE BASED SYSTEMS; MANAGEMENT; ORGANIC ACIDS;

BIOLOGICAL SEQUENCES; COMPLETE GENOMES; COMPREHENSIVE ANALYSIS; COMPUTATIONAL APPLICATIONS; DATA PRODUCTS; DO-MAINS; DOMAIN ANALYSES; DOMAIN ARCHITECTURES; EXPONENTIAL GROWTHS; GENE FUNCTIONS; GENE INTERACTIONS; GENE LEVELS; GENE PRODUCTS; HIGH THROUGHPUTS; INTEGRATION EFFORTS; INTRASPECIES VARIATIONS; PERFORMANCE DATUMS; PROTEIN DATABASES; PROTEIN INTERACTIONS; PROTEIN SEQUENCES; WORKFLOWS;

PROTEINS;

EID: 47649107467     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375625     Document Type: Conference Paper

References (25)

1. [Altintas,2004] I. Altintas, C. Berkley, E. Jaeger, M. Jones, B. Ludäscher, S. Mock. System demonstration, 16th Intl. Conf. on Scientific and Statistical Database Management (SSDBM'04), 21-23 June 2004, Santorini Island, Greece. http://www.kepler-project.org/
2. [Altshul,1997] Altshul S.F., Madden T.L., Schaffer A.A., Zhang J.H., Zhang Z., Miller W., Lipman D.J.. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acid Res, 25: 3389-3402,1997
3. [Apweiler,2001] Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001 29:37-40, 2001
4. [Björklund,2005] Björklund Å. K., Ekman D., Light S., Frey-Skött J. and Elofsson A. Domain Rearrangements in Protein Evolution Journal of Molecular Biology 353:911-923, 2005
5. [Blatecky,2005] Blatecky A., Gamiel K., Ramakrishnan L., Reed D.A., and Reed M. Building the Bioscience Gateway, Global Grid Forum Technical Paper, June 2005.
6. [Elsik 2007] Elsik C.G., Mackey A. J., Reese J. T., Milshina M. V., Roos, D. S., and Weinstock, G. M. Creating a honeybee consensus gene set Genome Biology 8:R13 [EMBL-EBI, 2007] (http://www.ebi.ac.uk/InterProScan/)
7. [Foster,2001] Foster I., Kesselman C., Tuecke S. The Anatomy of the Grid: Enabling Scalable Virtual Organizations International J. Supercomputer Applications, 15(3), 2001.
8. [Foster,2006] Foster I. Globus Toolkit Version 4: Software for Service-Oriented Systems. IFIP International Conference on Network and Parallel Computing, Springer-Verlag LNCS 3779, pp 2-13, 2006. http://www.globus.org
9. [Gropp, 1994] Gropp W., Lusk E., Skjellum A., Using MPI: Portable Parallel Programming with the Message-Passing Interface, MIT Press, 1994
10. [Kandaswamy,2006] Kandaswamy G., Fang L., Huang Y., Shirasuna S., Marru S., and Gannon D. Building Web Services for Scientific Grid Applications. IBM Journal of Research and Development, 50(2/3):249-260,2006
11. [Laszewski, 2000] von Laszewski, G., Foster, I., and Gawor, J. 2000. CoG kits: a bridge between commodity distributed computing and high-performance grids. In Proceedings of the ACM 2000 Conference on Java Grande (San Francisco, California, United States, June 03-04, 2000). JAVA '00. ACM Press, New York, NY, 97-106.
12. [Majithia,2004] Majithia S. Shields M.S.,Taylor I.J. and Wang I. Triana: A Graphical Web Service Composition and Execution Toolkit. In Proceedings of the IEEE International Conference on Web Services (ICWS'04), pages 514-524. IEEE Computer Society, 2004. http://www.trianacode.org/
13. [Mulder,2005] Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., Copley R., Courcelle E., Das U., Durbin R., Fleischmann W., Gough J., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya A.N., Orchard S., Pagni M., Ponting C.P., Quevillon E., Selengut J., Sigrist C.J., Silventoinen V., Studholme D.J., Vaughan R., Wu C.H. (2005). InterPro, progress and status in 2005. Nucleic Acids Res. 33, Database lssue:D201-5.
14. [Neuwald,2004] Neuwald A.F. and Liu. J.S. Gapped alignment of protein sequence motifs through Monte Carlo optimization of a Hidden Markov model. BMC Bioinformatics 2004, 5:157
15. [Oinn,2004] Oinn,T., Addis,M., Ferris,J., Marvin,D., Greenwood,M., Carver,T., Pocock,M.R., Wipat,A. and Li,P. (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 20, 3045-3054
16. [Ramakrishnan,2006] Ramakrishnan L., Reed M.S.C., Tilson J.L., Reed D.A.. Grid Portals for Bioinformatics, Second International Workshop on Grid Computing Environments (GCE), Workshop at SCI06, November 2006, Tampa, Florida
17. [RENCI,2004] Renaissance Computing Institute. Founded in 2004, the Renaissance Computing Institute (RENCI) is a major collaborative venture of Duke University, North Carolina State University, the University of North Carolina at Chapel Hill and the state of North Carolina. http://www.renci.org
18. [RENCI,2006] 9.21.06 /GRIDToday/ *RENCI BioPortal Enhanced With First Workflow* Full Story 〈http://www.gridtoday.com/grid/914377. html〉
19. [Ruta 2003] Ruta V., Jiang Y., Lee A., Chen J. and MacKinnon R. Functional analysis of an archaebacterial voltage-dependent K+ channel Nature 422:180-185. 2003.
20. [Shannon,2003] Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., and Ideker T. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Genome Res., Nov 2003; 13: 2498-2504.
21. [Tasneem,2005] Tasneem A., Iyer L.M., Jakobsson E., Aravind L. 2005 Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol. 2005; 6(1):R4
22. [Vlasblom,2006] Vlasblom J., Wu S., Pu S., Superina M., Liu G., Orsi C., Wodak S.J. GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks. Bioinformatics. 2006 Sep 1 ;22(17):2178-9.
23. [Wang,2006] Wang M. and Caetano-Anollés G. 2006 Global Phylogeny Determined by the Combination of Protein Domains in Proteomes Molecular Biology and Evolution 2006:2444-2454
24. [Zdobnov,2001] Zdobnov E.M., Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001 Sep;1 7(9):847-8.
25. [Zhang, 2003] Ng S., Zhang Z., Tan S. and Lin K. (2003) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res., 31, 251-254., 2003.