Protein multiple sequence alignment by hybrid bio-inspired algorithms

Nucleic Acids Research

Volumn 39, Issue 6, 2011, Pages 1980-1992

  Cutello, Vincenzo ^a   Nicosia, Giuseppe ^a   Pavone, Mario ^a   Prizzi, Igor ^a  

^a UNIVERSITY OF CATANIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CLONING; DATA BASE; GENETIC ALGORITHM; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; METHODOLOGY; PHYLOGENETIC TREE; PRIORITY JOURNAL; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOMATIC HYPERMUTATION;

ALGORITHMS; MODELS, IMMUNOLOGICAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 79953703445     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1052     Document Type: Review

References (61)

1. Eidhammer,I., Jonassen,I. and Taylor,W.R. (2004) Protein Bioinformatics. Wiley, Chichester, West Sussex, UK.
2. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (2004) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
3. Notredame,C. (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput. Biol., 3, 1405-1408.
4. Thompson,J.D., Plewniak,F., Ripp,R., Thierry,J.C. and Poch,O. (2001) Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 301, 937-951.
5. Altschul,S.F. and Lipman,D.J. (1989) Trees stars and multiple biological sequence alignment. SIAM J. Appl. Math., 49, 197-209.
6. Altschul,S.F., Carroll,R.J. and Lipman,D.J. (1989) Weights for data related by a tree. J. Mol. Biol., 207, 647-653.
7. Cutello,V., Nicosia,G., Pavone,M. and Prizzi,I. (2007) Proteomic multiple sequence alignments: refinement using an immunological local search. Applied and Industrial Mathematics in Italy, series on Advanced in Mathematics for Applied Sciences, World Scientific, Vol. 75, pp. 291-302.
8. Lones,M.A. and Tyrrell,A.M. (2007) Regulatory motif discovery using a population clustering evolutionary algorithm. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 4, pp. 403-414.
9. Bevilacqua,V., Menolascina,F., Alves,R.T., Tommasi,S., Mastronardi,G., Delgado,A., Paradiso,M.R., Nicosia,G. and Freitas,A.A. (2008) Artificial immune systems in Bioinformatics. In Smolinski,T.G., Milanova,M.G. and Hassanien,A. (eds), Computational Intelligence in Biomedicine and Bioinformatics: Current Trends and Applications. Springer, New York, NY, USA, pp. 305-330.
10. Cutello,V., Nicosia,G. and Pavone,M. (2007) An immune algorithm with stochastic aging and kullback entropy for the chromatic number problem. J. Combi. Optimi., 14, 9-33.
11. Cutello,V., Nicosia,G., Pavone,M. and Timmis,J. (2007) An immune algorithm for protein structure prediction on lattice models. IEEE Trans. Evol. Comput., 11, 101-117.
12. Bonizzoni,P. and Vedova,G.D. (2001) The complexity of multiple sequence alignment with SP-score that is a metric. Theor. Comput. Sci., 259, 63-79.
13. Wang,L. and Jiang,T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
14. Garey,M.R. and Johnson,D.S. (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman, New York.
15. Gupta,S.K., Kececioglu,J.D. and Schaffer,A. (1995) Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comput. Biol., 459-472.
16. Joo,K., Lee,J., Kim,I., Lee,S.-J. and Lee,J. (2008) Multiple sequence alignment by conformational space annealing. Biophys. J., 95, 4813-4819.
17. Lu,Y. and Sze,S.-H. (2008) Multiple sequence alignment based on profile alignment of intermediate sequences. J. Comput. Biol., 15, 767-777.
18. Rausch,T., Emde,A.-K., Weese,D., Döring,A., Notredame,C. and Reinert,K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24, i187-i192.
19. Löytynoja,A. and Goldman,N. (2008) A model of evolution and structure for multiple sequence alignment. Philos. Tran. R. Soc. Lond. B, Biol. Sci., 363, 3913-3919.
20. Corpet,F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
21. Devereux,J., Haeberli,P. and Smithies,O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res., 387-395.
22. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 24, 4876-4882. (Pubitemid 28022245)
23. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. (Pubitemid 24354800)
24. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate Multiple Sequence Alignment. J. Mol. Biol., 302, 205-217.
25. Smith,R.F. and Smith,T.F. (1992) Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng., 5, 35-41.
26. Zhou,H. and Zhou,Y. (2005) SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics, 21, 3615-3621. (Pubitemid 41264096)
27. Do,C.B., Mahabhashyam,M.S.P., Brudno,M. and Batzoglou,S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340. (Pubitemid 40309398)
28. Carrillo,H. and Lipman,D.J. (1988) The multiple sequence alignment problem in biology. SIAM J. Appl. Math., 48, 1073-1082.
29. Stoye,J., Moulton,V. and Dress,A.W. (1997) DCA: an efficient implementation of the divide-and conquer approach to simultaneous multiple sequence alignment. Bioinformatics, 13, 625-626. (Pubitemid 28039660)
30. Morgenstern,B., Frech,K., Dress,A. and Werner,T. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294. (Pubitemid 28395866)
31. Morgenstern,B., Frech,K., Dress,A. and Werner,T. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
32. Gotoh,O. (1994) Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Bioinformatics., 10, 379-387.
33. Eddy,S.R. (1995) Multiple alignment using hidden Markov models. 3rd International Conference on Intelligent Systems for Molecular Biology, Vol. 3, pp. 114-120.
34. Edgar,R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
35. Notredame,C. and Higgins,D.G. (1996) SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res., 24, 1515-1539.
36. Notredame,C. (1998) COFFEE: an objective function for multiple sequence alignments. Bioinformatics, 14, 407-422.
37. Simossis,V.A. and Heringa,J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res., 33, 289-294.
38. Shyu,C., Sheneman,L. and Foster,J.A. (2004) Multiple sequence alignment with evolutionary computation. Genetic Prog. Evol. Mach., 5, 121-144.
39. Nguyen,H.D., Yoshihara,I., Yamamori,K. and Yasunaga,M. (2002) Aligning multiple protein sequences by parallel hybrid genetic algorithm. Genome Inform., 13, 123-132.
40. Cutello,V. and Nicosia,G. (2006) A clonal selection algorithm for coloring, hitting set and satisfiability problems. International Workshop on Natural and Artificial Immune Systems (NAIS), Vol. 3931 of LNCS, Springer, pp. 324-337.
41. Cutello,V., Narzisi,G., Nicosia,G. and Pavone,M. (2006) An immunological algorithm for global numerical optimization. 7th International Conference on Artificial Evolution (EA), Vol. 3871 of LNCS, Springer, pp. 284-295.
42. Cutello,V., Lee,D., Leone,S., Nicosia,G. and Pavone,M. (2006) Clonal selection algorithm with dynamic population size for bimodal search spaces. 2nd International Conference on Natural Computaion (ICNC), Vol. 4221 of LNCS, Springer, pp. 949-958.
43. Cutello,V., Lee,D., Nicosia,G., Pavone,M. and Prizzi,I. (2006) Aligning multiple protein sequences by hybrid clonal selection algorithm with insert-remove-gaps and blockshuffling operators. 5th International Conference on Artificial Immune Systems (ICARIS), Vol. 4163 of LNCS, Springer, pp. 13-28.
44. Cutello,V., Nicosia,G. and Pavone,M. (2003) A hybrid immune algorithm with information gain for the graph coloring problem. Genetic and Evolutionary Computaion COnference (GECCO), Vol. 2723 of LNCS, Springer, pp. 171-182.
45. Cutello,V., Narzisi,G., Nicosia,G. and Pavone,M. (2005) Clonal selection algorithms: a comparative case study using effective mutation potentials. 4th International Conference on Artificial Immune Systems (ICARIS), Vol. 4163 of LNCS, Springer, pp. 13-28.
46. Cutello,V., Morelli,G., Nicosia,G. and Pavone,M. (2005) Immune algorithms with aging operators for the string folding problem and the protein folding problem. 5th European Conference on Comput.ion in Combinatorial Optimization (EvoCOP), Vol. 3448 of LNCS, Springer, pp. 80-90.
47. Cutello,V., Nicosia,G. and Pavone,M. (2004) Exploring the capability of immune algorithms: a characterization of hypermutation operators. 3rd International Conference on Artificial Immune Systems (ICARIS), Vol. 3239, of LNCS, Springer, pp. 263-276 (2004).
48. Cutello,V., Nicosia,G. and Pavone,M. An immune algorithm with hyper-macromutations for the dill's 2d hydrophobic-hydrophilic model. Cong. Evol. Comput., 1, 1074-1080.
49. Cutello,V., Nicosia,G., Pavone,M. and Narzisi,G. (2006) Real coded clonal selection algorithm for unconstrained global numerical optimization using a hybrid inversely proportional hypermutation operator. 21st Annual ACM Symposium on Applied Computing (SAC), Vol. 2, ACM, 950-954.
50. Thompson,J.D., Plewniak,F. and Poch,O. (1999) BALIBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88. (Pubitemid 29101202)
51. Bahr,A., Thompson,J.D., Thierry,J.C. and Poch,O. (2001) BALIBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29, 232-326.
52. Thompson,J.D., Koehl,P., Ripp,R. and Poch,O. (2005) BALIBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins Struct. Funct. Bioinformatics, 61, 127-136.
53. Castrogiovanni,M., Nicosia,G. and Rascuna,R. (2007) Experimental analysis of the aging operator for static and dynamic optimisation problems. 11th International Confernce on Knowledge-Based and Intelligent Information and Engineering Systems - KES 2007, Vietri sul Mare, Italy. Springer, Vol. 4694 of LNCS, pp. 804-811.
54. Pei,J., Sadreyev,R. and Grishin,N.V. (2003) PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics, 19, 427-428. (Pubitemid 36284945)
55. Papadopoulos,J.S. and Agarwala,R. (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23, 1073-1079. (Pubitemid 47050558)
56. Russell,D.J., Out,H.H. and Sayood,K. (2008) Grammar-based distance in progressive multiple sequence alignment. BMC Bioinformatics, 9.
57. Ge,H., Zhong,W., Du,W., Qian,F. and Wang,L. (2007) A hybrid algorithm based on artificial immune system and hidden markov model for multiple sequence alignment. International Conference on Intelligent Systems and Knowledge Engineering (ISKE 2007). Atlantis Press.
58. Layeb,A. and Deneche,A.H. (2007) Multiple sequence alignment by immune artificial system. ACS/IEEE International Conference on Computer Systems and Applications, pp. 336-342.
59. Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier trasform. Nucleic Acids Res., 30, 3059-3066. (Pubitemid 34851225)
60. Lassmann,T. and Sonnhammer,E. (2005) Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics., 6.
61. Sze,S., Lu,Y. and Yang,Q. (2006) a polynomial time solvable formulation of multiple sequence alignment. J. Comput. Biol., 13, 309-319.