A new pheromone trail-based genetic algorithm for comparative genome assembly

Nucleic Acids Research

Volumn 36, Issue 10, 2008, Pages 3455-3462

  Zhao, Fangqing ^a   Zhao, Fanggeng ^b   Li, Tao ^a   Bryant, Donald A ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Vehicle Management Institute   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; PHEROMONE;

ACCURACY; ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; INTERNET; NONHUMAN; PRIORITY JOURNAL; SIMULATION; ALGORITHM; COMPUTER SIMULATION; CONTIG MAPPING; EVALUATION; GENOMICS;

BACTERIA (MICROORGANISMS);

ALGORITHMS; COMPUTER SIMULATION; CONTIG MAPPING; GENOME, BACTERIAL; GENOMICS;

EID: 45549101719     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn168     Document Type: Article

References (22)

1. van Hijum,S.A., Zomer,A.L., Kuipers,O.P. and Kok,J. (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res., 33, W560-W566.
2. Pop,M., Phillippy,A., Delcher,A.L. and Salzberg,S.L. (2004) Comparative genome assembly. Brief. Bioinform., 5, 237-248.
3. Richter,D.C., Schuster,S.C. and Huson,D.H. (2007) OSLay: Optimal syntenic layout of unfinished assemblies. Bioinformatics, 23 1573-1579.
4. Holland,J.H. (1992) Genetic algorithms. Sci. Amer., 4, 44-50.
5. Nguyen,H.D., Yoshihara,I., Yamamori,K. and Yasunaga,M. (2002) Aligning multiple protein sequences by parallel hybrid genetic algorithm. Gen. Inform., 13, 123-132.
6. Kikuchi,S., Tominaga,D., Arita,M., Takahashi,K. and Tomita,M. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics, 19, 643-650.
7. Gilman,A. and Ross,J. (1995) Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model. Biophy. J. 69, 1321-1333.
8. Ooi,C.H. and Tan,P. (2003) Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. Bioinformatics 19, 37-44.
9. Lewis,P.O. (1998) A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol., 15 277-283.
10. Kosakovsky Pond,S.L., Posada,D., Gravenor,M.B., Woelk,C.H. and Frost,S.D. (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol., 23, 1891-1901.
11. Syswerda,G. (1991) A study of reproduction in generational and steady-state genetic algorithms. In Foundations of Genetic Algorithms Morgan Kauffmann Publishers. San Mateo, USA, pp. 94-101.
12. Shtovba,S.D. (2005) Ant algorithms: Theory and applications. Program. Comp. Soft., 4, 167-178.
13. Whitley,D. (1989) The GENITOR algorithm and selection pressure: Why rank-based allocation of reproductive trials is best. Proceedings of the Third International Conference on Genetic Algorithms, 116-121.
14. Dorigoa,M. and Blum,C. (2005) Ant colony optimization theory: A survey. Theor. Comp. Sci., 344, 243-278.
15. Heidelberg,J.F., Paulsen,I.T., Nelson,K.E., Gaidos,E.J., Nelson,W.C., Read,T.D., Eisen,J.A., Seshadri,R., Ward,N., Methe,B. et al. (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol., 20, 1118-1123.
16. Stakweather,T., McDaniel,S., Mathias,K., Whitley,C. and Whitley,D. (1991) A comparison of genetic sequencing operators. In Proceedings of the 4th International Conference on Genetic Algorithms. Morgan Kauffmann Publishers, San Mateo, USA, pp. 69-76.
17. Yu,Z., Li,T., Zhao,J. and Luo,J. (2002) PGAAS: A prokaryotic genome assembly assistant system. Bioinformatics, 18, 661-665.
18. Frangeul,L., Glaser,P., Rusniok,C., Buchrieser,C., Duchaud,E., Dehoux,P. and Kunst,F. (2004) CAAT-Box, contigs-assembly and annotation tool-box for genome sequencing projects. Bioinformatics, 20, 790-797.
19. Rocap,G., Larimer,F.W., Lamerdin,J., Malfatti,S., Chain,P., Ahlgren,N.A., Arellano,A., Coleman,M., Hauser,L., Hess,W.R. et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424, 1042-1047.
20. Palenik,B., Brahamsha,B., Larimer,F.W., Land,M., Hauser,L., Chain,P., Lamerdin,J., Regala,W., Allen,E.E., McCarren,J. et al. (2003) The genome of a motile marine Synechococcus. Nature, 424, 1037-1042.
21. Green,P. (2007) 2 × genomes - does depth matter? Genome Res., 17, 1547-1549.
22. Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J., Chen,Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.