A Multiobjective Variable Neighborhood Search for Solving the Motif Discovery Problem

Advances in Intelligent and Soft Computing

Volumn 73 AISC, Issue , 2010, Pages 39-46

  González álvarez, David L ^a   Vega Rodríguez, Miguel A ^a   Gómez Pulido, Juan A ^a   Sánchez Pérez, Juan M ^a  

^a UNIVERSITY OF EXTREMADURA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; EVOLUTIONARY ALGORITHMS; OPTIMIZATION;

COMPLETE SOLUTIONS; EVOLUTIONARY TECHNIQUES; HYPERVOLUME INDICATORS; MOTIF DISCOVERY; MULTI OBJECTIVE; MULTI-OBJECTIVE EVOLUTIONARY; MULTI-OBJECTIVE VARIABLE NEIGHBORHOOD SEARCHES; TRAJECTORY-BASED; VARIABLE NEIGHBORHOOD SEARCH;

DNA SEQUENCES;

EID: 85038026212     PISSN: 18675662     EISSN: 18600794     Source Type: Book Series    
DOI: 10.1007/978-3-642-13161-5_6     Document Type: Conference Paper

References (10)

1. Stine, M., Dasgupta, D., Mukatira, S.: Motif discovery in upstream sequences of co-ordinately expressed genes. In: The 2003 Congress on Evolutionary Computation (CEC 2003), December 2003, vol. 3, pp. 1596–1603 (2003)
2. Kaya, M.: Motif discovery using multi-objective genetic algorithm in biosequences. In: Berthold, M., Shawe-Taylor, J., Lavrač, N. (eds.) IDA 2007. LNCS, vol. 4723, pp. 320–331. Springer, Heidelberg (2007)
3. Mladenovic, N., Hansen, P.: Variable neighborhood search. Computers and Operations Research 24, 1097–1100 (1997)
4. Fonseca, C.M., Paquete, L., Lopez–Ibanez, M.: An improved dimension–sweep algorithm for the hypervolume indicator. In: IEEE Congress on Evolutionary Computation (CEC 2006), July 2006, pp. 1157–1163 (2006)
5. Tompa, M., et al.: Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1), 137–144 (2005)
6. Wingender, E., Dietze, P., Karas, H., Knüppel, R.: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 24(1), 238–241 (1996)
7. Kaya, M.: MOGAMOD: Multi–objective genetic algorithm for motif discovery. Expert Systems with Applications: An International Journal 36(2), 1039–1047 (2009)
8. Roth, F.P., Hughes, J.D., Estep, P.W., Church, G.M.: Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole genome mRNA quantitation. Nature Biotechnology 16(10), 939–945 (1998)
9. Bailey, T.L., Elkan, C.: Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21(1-2), 51–80 (1995)
10. Pavesi, G., Mereghetti, P., Mauri, G., Pesole, G.: Weeder Web: discovery of transcription factor binding sites in a set of sequences from co–regulared genes. Nucleic Acids Research 32, 199–203 (2004)