Genetic Sequence Classification and its Application to Cross-species Homology Detection

Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology

Volumn 35, Issue 3, 2003, Pages 273-285

  Mukhopadhyay, Snehasis ^a   Tang, Changhong ^a   Huang, Jeffery ^a   Palakal, Mathew ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Artificial neural network; Clustering; Cross species homology detection; Sequence alignment; Sequence classification; Unsupervised and supervised learning

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; GENES; NEURAL NETWORKS;

SEQUENCE CLASSIFICATION;

SIGNAL PROCESSING;

EID: 0141921565     PISSN: 13875485     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:VLSI.0000003025.42408.40     Document Type: Conference Paper

References (30)

1. A. J. Enright and C.A. Ouzounis, "GeneRAGE: A Robust Algorithm for Sequence Clustering and Domain Detection," Bioinformatics, vol. 16, no. 5, 2000, pp. 451-457.
2. M.D. Adams et al., "Complementary DNA Sequencing: Expressed Sequence Tags and the Human Genome Project," Science, vol. 252, 1991, pp. 1651-1656.
3. G.N. Lance and W.T. Williams, "Computer Programs for Hierarchical Polythetic Classification," Comput. J., vol. 9, 1966, pp. 60-64.
4. P.H.A. Sneath, "The Application of Computers to Taxonomy," J. Gen. Microbiol., vol. 17, 1957, pp. 201-226.
5. S.C. Johnson, "Hierarchical Clustering Schemes," Psychometrika, vol. 32, 1967, pp. 241-254.
6. J.H. Ward, "Hierarchical Grouping to Optimize an Objective Function," J. Am. Statist. Ass., vol. 58, 1963, pp. 236-244.
7. J. MacQueen, "Some Methods for Classification and Analysis of Multivariate Observations," Proc. 5th Berkeley Symp. Math. Stat. Probab., vol. 1, 1965, pp. 281-297.
8. J. Herrero, A. Valencia, and J. Dopazo, "A Hierarchical Unsupervised Growing Neural Network for Clustering Gene Expression Patterns," Bioinformatics, vol. 17, no. 2, 2000, pp. 126-136.
9. A.V. Lukashin and R. Fuchs, "Analysis of Temporal Gene Expression Profiles: Clustering by Simulated Annealing and Determining the Optimal Number of Clusters," Bioinformatics, vol. 17, no. 5, 2001, pp. 405-414.
10. P. Baccam, R.J. Thompson, O. Fedrigo, S. Carpenter, and J.L. Cornette, "PAQ: Partition Analysis of Quasispecies," Bioinformatics, vol. 17, no. 1, 2001, pp. 16-22.
11. A. Krause and M. Vingron, "A Set-Theoretic Approach to Database Searching and Clustering," Bioinformatics, vol. 14, no. 5, 1998, pp. 430-438.
12. C. Wu, G. Whitson, J. McLarty, A. Ermongkonchai, and T.C. Chang, "Protein Classification Artificial Neural System," Protein Science, vol. 1, 1992, pp. 667-677.
13. M. Milik, A. Kolinski, and J. Skolnick, "Neural Network System for the Evaluation of Side-Chain Packing in Protein Structures," Protein Eng., vol. 8, 1995, pp. 225-236.
14. S. Mukhopadhyay, C. Tang, J. Huang, M. Yu, and M. Palakal, "A Comparative Study of Genetic Sequence Classification Algorithms," Proceedings of IEEE Neural Networks in Signal Processing (NNSP) Conference, 2002, pp. 57-66.
15. S.B. Needleman and C.D. Wunsch, "A General Method Applicable to the Search for Similarities in the Amino Acid Sequences of Two Proteins," J. Mol. Biol., vol. 48, 1970, pp. 443-453.
16. T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences," J. Mol. Biol., vol. 147, 1981, pp. 195-197.
17. W.R. Perason and D.J. Lipman, "Improved Tools for Biological Sequence Comparision," Proc. Natl. Acad. Sci. USA, vol. 85, 1988, pp. 244-2448.
18. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman, "Basic Local Alignment Search Tool," J. Mol. Biol., vol. 215, 1990, pp. 403-410.
19. M.S. Waterman and M. Eggert, "A New Algorithm for Subsequence Alignments with Application to tRNA-rRNA Comparisons," J. Mol. Biol., vol. 197, 1987, pp. 723-728.
20. J.T. Tou and R.C. Gonazalez, Pattern Recognition Principles, pp. 92-94, 1974.
21. J. Mostafa, S. Mukhopadhyay, W. Lam, and M. Palakal, "A Multilevel Approach to Intelligent Information Filtering: Model, System and Evaluation," ACM Transactions on Information Systems, vol. 15, no. 4, 1997, pp. 368-399.
22. S. Hayin, Neural Networks: A Comprehensive Foundation, New York: Macmillan, 1994.
23. UniGene, http://www.ncbi.nlm.nih.gov/UniGene
24. G.D. Schuler et al., "A Gene Map of the Human Genome," Science, vol. 274, 1996, p. 540.
25. Z. Zhang, S. Schwarz, L. Wagner, and W. Miller, "A Greedy Algorithm for Aligning DNA Sequences," J. Comp. Biol., vol. 7, 2000, pp. 203-214.
26. SP System, http://sp-www.iu.edu
27. OpenMP API: http://www.openmp.org
28. W. Fleischmann, S. Moller, A. Gateau, and R. Apweiler, "A Novel Method for Automatic Functional Annotation of Proteins," Bioinformatics, vol. 15, no. 3, 1999, pp. 228-233.
29. R.D. King, A. Karwath, A. Clare, and L. Dehaspe, "The Utility of Different Representation of Protein Sequence for Predicting Functional Class," Bioinformatics, vol. 17, no. 5, 2001, pp. 445-454.
30. P. Pavlidis, J. Weston, J. Cai, and W.N. Grundy, "Gene Functional Classification from Heterogeneous Data," ACM Trans., 2001, pp. 249-255.