Finding patterns in protein sequences by using a hybrid multiobjective teaching learning based optimization algorithm

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 12, Issue 3, 2015, Pages 656-666

  González Álvarez, David L ^a   Vega Rodríguez, Miguel A ^a   Rubio Largo, Álvaro ^a  

^a UNIVERSITY OF EXTREMADURA   (Spain)

Author keywords

Hybrid algorithm; Multiobjective optimization; PROSITE; Proteins; Teaching learning based optimization

Indexed keywords

ALGORITHMS; BIOINFORMATICS; LEARNING ALGORITHMS; OPTIMIZATION; PROTEINS;

BIOLOGICAL FUNCTIONS; BIOLOGICAL INFORMATION; HYBRID ALGORITHMS; LOCAL SEARCH FUNCTION; PROSITE; PROTEIN FUNCTIONS; PROTEIN SEQUENCES; TEACHING-LEARNING-BASED OPTIMIZATIONS;

MULTIOBJECTIVE OPTIMIZATION;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; PROCEDURES; PROTEIN DATABASE; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84940397323     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2014.2369043     Document Type: Article

References (40)

1. P. Bork and E. V. Koonin, "Protein sequence motifs," Current Opinion Struct. Biol., Vol. 6, no. 3, pp. 366-376, 1996.
2. K. Deb, Multi-Objective Optimization Using Evolutionary Algorithms. Hoboken, NJ, USA: Wiley, 2001.
3. R. V. Rao, V. J. Savsani, and D. P. Vakharia, "Teaching-learning-based optimization: A novel method for constrained mechanical design optimization problems," Comput.-Aided Des., Vol. 43, no. 3, pp. 303-315, 2011.
4. T. Niknam, R. Azizipanah-Abarghooee, and J. Aghaei, "A new modified teaching-learning algorithm for reserve constrained dynamic economic dispatch," IEEE Trans. Power Syst., Vol. 28, no. 2, pp. 749-763, May 2013.
5. P. Roy, "Teaching learning based optimization for short-term hydrothermal scheduling problem considering valve point effect and prohibited discharge constraint," Int. J. Elect. Power & Energy Syst., Vol. 53, pp. 10-19, 2013.
6. E.-G. Talbi, Metaheuristics: From Design to Implementation. Wiley Publishing, 2009, ISBN: 0470278587, 9780470278581.
7. C. Sigrist, E. de Castro, L. Cerutti, B. Cuche, N. Hulo, A. Bridge, L. Bougueleret, and I. Xenarios, "New and continuing developments at PROSITE," Nucleic Acids Res., Vol. 41 (Database issue), pp. D344-347, 2012.
8. T. L. Bailey, M. Bodn, F. Buske, M. Frith, C. Grant, L. Clementi, J. Ren, W. Li, and W. Noble, "MEME SUITE: Tools for motif discovery and searching," Nucleic Acids Res., Vol. 37, no. 2, pp. W202-W208, 2009.
9. W. Thompson, L. Newberg, S. Conlan, L. McCue, and C. Lawrence, "The gibbs centroid sampler," Nucleic Acids Res., Vol. 35 (Web Server issue), pp. W232-237, 2007.
10. G. Z. Hertz and G D. Stormo, "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences," Bioinformatics, Vol. 15, no. 7-8, pp. 563-577, 1999.
11. J. van Helden, B. Andre, and J. Collado-Vides, "Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies," J. Molecular Biol., Vol. 281, no. 5, pp. 827-842, 1998.
12. J. van Helden, A. F. Rios, and J. Collado-Vides, "Discovering regulatory elements in non-coding sequences by analysis of spaced dyads," Nucleic Acids Res., Vol. 28, no. 8, pp. 1808-1818, 2000.
13. E. Eskin and P. A. Pevzner, "Finding composite regulatory patterns in DNA sequences," Bioinformatics, Vol. 18 (Suppl 1), pp. S354-S363, 2002.
14. S. Sinha and M. Tompa, "YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation," Nucleic Acids Res., Vol. 31, no. 13, pp. 3586-3588, 2003.
15. M. Regnier and A. Denise, "Rare events and conditional events on random strings," Discrete Math. Theoretical Comput. Sci., Vol. 6, pp. 191-214, 2004.
16. G. Pavesi, P. Mereghetti, F. Zambelli, M. Stefani, G Mauri, and G Pesole, "MoD Tools: Regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes," Nucleic Acids Res., Vol. 34, pp. W566-W570, 2006.
17. J. D. Hughes, P. W. Estep, S. Tavazoie, and G M. Church, "Computational identification of CIS-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae," J. Molecular Biol., Vol. 296, no. 5, pp. 1205-1214, 2000.
18. C. T. Workman and G D. Stormo, "ANN-Spec: A method for discovering transcription factor binding sites with improved specificity," in Proc. Pacific Symp. Biocomput., 2000, pp. 467-478.
19. G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, P. Rouze, and Y. Moreau, "A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling," Bioinformatics, Vol. 17, no. 12, pp. 1113-1122, 2001.
20. M. C. Frith, U. Hansen, J. L. Spouge, and Z. Weng, "Finding functional sequence elements by multiple local alignment," Nucleic Acids Res., Vol. 32, no. 1, pp. 189-200, 2004.
21. A. V. Favorov, M. S. Gelfand, A. V. Gerasimova, D. A. Ravcheev, A. A. Mironov, and V. J. Makeev, "A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length," Bioinformatics, Vol. 21, no. 10, pp. 2240-2245, 2005.
22. J. H. Holland, Adaptation in Natural and Artificial Systems. Ann Arbor, MI, USA: Univ. of Michigan Press, 1975.
23. F. F. M. Liu, J. J. P. Tsai, R. M. Chen, S. N. Chen, and S. H. Shih, "FMGA: Finding motifs by genetic algorithm," in Proc. 4th IEEE Symp. Bioinform. Bioeng., 2004, pp. 459-466.
24. C. Notredame and D. G. Higgins, "SAGA: Sequence alignment by genetic algorithm," Nucleic Acids Res., Vol. 24, no. 8, pp. 1515-1524, 1996.
25. M. Stine, D. Dasgupta, and S. Mukatira, "Motif discovery in upstream sequences of coordinately expressed genes," in Proc. Congress Evol. Comput, 2003, vol. 3, pp. 1596-1603.
26. Y. Che, D. Song, and K. Rashedd, "MDGA: Motif discovery using a genetic algorithm," in Proc. Conf. Genetic Evol. Comput., 2005, pp. 447-452.
27. Z. Wei and S. Jensen, "GAME: Detecting CIS-regulatory elements using a genetic algorithm," Bioinformatics, Vol. 22, no. 13, pp. 1577-1584, 2006.
28. T.-K. Chan, K.-S. Leung, and K.-H. Lee, "TFBS identification based on genetic algorithm with combined representations and adaptive post-processing," Bioinformatics, Vol. 24, no. 3, pp. 341-349, 2008.
29. T.-K. Chan, G. Li, K.-S. Leung, and K.-H. Lee, "Discovering multiple realistic TFBS motifs based on a generalized model," BMC Bioinform., Vol. 10, no. 1, pp. pp. 321-322, 2009.
30. L. Shao and Y. Chen, "Bacterial foraging optimization algorithm integrating tabu search for motif discovery," in Proc. IEEE Int. Conf. Bioinform. Biomed., 2009, pp. 415-418.
31. L. Shao, Y. Chen, and A. Abraham, "Motif discovery using evolutionary algorithms," in Proc. Int. Conf. Soft Comput. Pattern Recognit., 2009, pp. 420-425.
32. M. A. Lones and A. M. Tyrrell, "Regulatory motif discovery using a population clustering evolutionary algorithm," IEEE/ACM Trans. Comput. Biol. Bioinform., Vol. 4, no. 3, pp. 403-414, Jul.-Sep. 2007.
33. J. Park and S. Teichmann, "DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins," Bioinformatics, Vol. 14, no. 2, pp. 144-150, 1998.
34. A. Heger, C. Wilton, A. Sivakumar, and L. Holm, "ADDA: A domain database with global coverage of the protein universe," Nucleic Acids Res., Vol. 33, pp. D188-D191, 2005.
35. M. Fan, K.-C. Wong, T. Ryu, T. Ravasi, and X. Gao, "SECOM: A novel hash seed and community detection based-approach for genome-scale protein domain identification," PLoS ONE, Vol. 7, no. 6, p. e39475, 2012.
36. D. L. Gonzalez-Alvarez, M. A. Vega-Rodríguez, J. A. Gomez-Pulido, and J. M. Sanchez-Perez, "Predicting DNA motifs by using evolutionary multiobjective optimization," IEEE Trans. Syst., Man Cybern. Part C: Appl. Rev., Vol. 42, no. 6, pp. 913-925, Nov. 2012.
37. D. L. Gonzalez-Alvarez, M. A. Vega-Rodríguez, and A. Rubio-Largo, "Convergence analysis of some multiobjective evolutionary algorithms when discovering motifs," Soft Comput., Vol. 18, no. 5, pp. 853-869, 2014.
38. G. B. Fogel, D. G. Weekes, G Varga, E. R. Dow, H. B. Harlow, J. E. Onyia, and C. Su, "Discovery of sequence motifs related to coex-pression of genes using evolutionary computation," Nucleic Acids Res., Vol. 32, no. 13, pp. 3826-3835, 2004.
39. G. B. Fogel, V. W. Porto, G. Varga, E. R. Dow, A. M. Crave, D. M. Powers, H. B. Harlow, E. W. Su, J. E. Onyia, and C. Su, "Evolutionary computation for discovery of composite transcription factor binding sites," Nucleic Acids Res., Vol. 36, no. 21, pp. e142, 1-14, 2008.
40. G. E. Crooks, G Hon, J. M. Chandonia, and S. E. Brenner, "WebLogo: A sequence logo generator," Genome Res., Vol. 14, pp. 1188-1190, 2004.