A hybrid framework for protein sequence clustering and classification using signature motif information

Integrated Computer-Aided Engineering

Volumn 16, Issue 4, 2009, Pages 353-365

  Chen, Wei Bang ^a   Zhang, Chengcui ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCES; CLASSIFICATION ,; HIERARCHICAL AGGLOMERATIVE CLUSTERING; HYBRID CLUSTERING; HYBRID FRAMEWORK; PARTITION CLUSTERING; PHASE I; PHASE II; PROFILE HIDDEN MARKOV MODEL; PROTEIN SEQUENCE CLUSTERING; PROTEIN STRUCTURAL MOTIFS; SEQUENCE CLASSIFICATION; SEQUENCE SIMILARITY; THREE STAGES;

HIDDEN MARKOV MODELS;

EID: 70350515918     PISSN: 10692509     EISSN: None     Source Type: Journal    
DOI: 10.3233/ICA-2009-0323     Document Type: Article

References (19)

1. E. De Castro, C.J. Sigrist, A. Gattiker, V. Bulliard, P.S. Langendijk-Genevaux, E. Gasteiger, A. Bairoch and N. Hulo, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Research 34 (2006), W362-W365.
2. W.-B. Chen, C. Zhang and H. Zhong, An unsupervised protein sequences clustering algorithm using functional domain information, Proceedings of the 2008 IEEE International Conference on Information Reuse and Integration (IRI 2008), 2008, 76-81.
3. R. Durbin, S.R. Eddy, A. Krogh and G. Mitchison, Biological sequence analysis - probabilistic models of proteins and nucleic acids, Cambridge University Press, Cambridge, UK, 2000.
4. S.R. Eddy, Profile hidden Markov models, Bioinformatics 14 (1998), 755-763.
5. S.R. Eddy, Hidden Markov models, Current Opinion in Structural Biology 6 (1996), 361-365.
6. The EMBL-EBI Tools. (http://www.ebi.ac.uk/Tools/clustalw2 /index.html)
7. A.J. Enright and C.A. Ouzounis, GeneRAGE: a robust algorithm for sequence clustering and domain detection, Bioinformatics 16 (2000), 451-457.
8. M. Gribskov, A.D. McLachlan and D. Eisenberg, Profile Analysis: Detection of Distantly Related Proteins, Proceedings of the National Academy of Sciences of the United States of America (PNAS) 84 (1987), 4355-4358.
9. J. Han and M. Kamber, Data Mining: Concepts and Techniques, San Francisco, CA, USA: Morgan Kaufmann Publishers, 2001.
10. S. Henikoff and J.G. Henikoff, Amino Acid Substitution Matrices from Protein Blocks, Proceedings of the National Academy of Sciences of the United States of America (PNAS) 89 (1992), 10915-10919.
11. N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, B. Cuche, E. De Castro, C. Lachaize, P.S. Langendijk-Genevaux and C.J.A. Sigrist, The 20 years of PROSITE, Nucleic Acids Research 36 (2007), D245-D249.
12. E.V. Kriventseva, M. Biswas and R. Apweiler, Clustering and analysis of protein families, Current Opinion in Structural Biology 11 (2001), 334-339.
13. C.J. Ku and G. Yona, Domain-Based Protein Hierarchy and detection of semantically significant domain architectures, Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology, 2005.
14. W. Mahdi, S. Werda and A.B. Hamadou, A hybrid approach for automatic lip localization and viseme classification to enhance visual speech recognition, Integrated Computer-Aided Engineering (ICAE) 15 (2008), 253-266.
15. I.S. Main and I. Dubchak, Representing and reasoning about protein families using generative and discriminative methods, Journal of Computational Biology: a Journal of Computational Molecular Cell biology 7 (2000), 849-863.
16. C.J. Van Rijsbergen. Information Retrieval, Butterworths, London, 1979.
17. A. Rosenberg and J. Hirschberg, V-measure: a Conditional Entropy-Based External Cluster Evaluation Measure, Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, 2007, 410-420.
18. I. Rudolfov́a and J. Zendulka, Clustering of protein sequences, Proceedings of 1st International Workshop WFM'06, 2006, 71-78.
19. P.D. Thomas, M.J. Campbell, A. Kejariwal, H. Mi, B. Karlak, R. Daverman, K. Diemer, A. Muruganujan and A. Narechania, PANTHER: a library of protein families and subfamilies indexed by function, Genome Research 13 (2003), 2129-2141.