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A Practical Algorithm for the 2-Species Duplication-Loss Small Phylogeny Problem

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Intelligent Computing Theories and Application (ICIC 2016)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 9771))

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Abstract

In this paper, the 2-Species Duplication-Loss Small Phylogeny Problem is studied. By introducing an alignment algorithm, a labeling algorithm and three smart mutate operators, a genetic algorithm G2SP is presented. Algorithm G2SP adopts the method of combining the general operator and the smart ones. The general operator maintains the population diversity effectively, while the smart ones improve population convergence and make it evolve to the optimal solution more quickly. The tRNA and rRNA gene data of six kinds of real bacterium were used to test the performance of algorithms. The experimental results indicate that the G2SP algorithm can get fewer evolution cost than the PBLB algorithm proposed by Holloway et al., and it is an effective method for solving the 2-species duplication-loss small phylogeny problem.

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References

  1. Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: Shamir, R., Miyano, S., Istrail, S., Pevzner, P., Waterman, M. (eds.) RECOMB 2000, pp. 138–146. ACM Press, New York (2000)

    Google Scholar 

  2. Chauve, C., Doyon, J.P., El-Mabrouk, N.: Gene family evolution by duplication, speciation, and loss. J. Comput. Biol. 15(8), 1043–1062 (2008)

    Article  MathSciNet  Google Scholar 

  3. Berard, B., Szollosi, G.J., Daubin, V.: Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics 28, i382–i388 (2012)

    Article  Google Scholar 

  4. Patterson, M., Szöllösi, G., Daubin, V., Tannier, E.: Lateral gene transfer, rearrangement, reconciliation. BMC Bioinf. 14, S4 (2013)

    Article  Google Scholar 

  5. Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)

    Article  Google Scholar 

  6. Rogers, H.H., Bergman, C.M., Griffiths-Jones, S.: The evolution of tRNA genes in Drosophila. Genome Biol. Evol. 2, 467–477 (2010)

    Article  Google Scholar 

  7. Withers, M., Wernisch, L., Reis, M.D.: Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. Bioinformatics 12, 933–942 (2006)

    Google Scholar 

  8. Bermudez-Santana, C., Attolini, C.S., Kirsten, T., Engelhardt, J., Prohaska, S., Steigele, S., Stadler, P.: Genomic organization of eukaryotic tRNAs. BMC Genomics 11, 270 (2010)

    Article  Google Scholar 

  9. Tang, D., Glazov, E., McWilliam, S., Barris, W., Dalrymple, B.: Analysis of the complement and molecular evolution of tRNA genes in cow. BMC Genomics 10, 188 (2009)

    Article  Google Scholar 

  10. Holloway, P., Swenson, K., Ardell, D.H., et al.: Ancestral genome organization: an alignment approach. J. Comput. Biol. 20(4), 280–295 (2013)

    Article  MathSciNet  Google Scholar 

  11. Andreotti, S., Reinert, K., Canzar, S.: The duplication-loss small phylogeny problem: from cherries to trees. J. Comput. Biol. 20(9), 643–659 (2013)

    Article  MathSciNet  Google Scholar 

  12. Dondi, R., El-Mabrouk, N.: Aligning and labeling genomes under the duplication-loss model. In: Bonizzoni, P., Brattka, V., Löwe, B. (eds.) CiE 2013. LNCS, vol. 7921, pp. 97–107. Springer, Heidelberg (2013)

    Google Scholar 

  13. Tremblay-Savard, O., Benzaid, B., Lang, B.F., El-Mabrouk, N.: Evolution of tRNA repertoires in bacillus inferred with OrthoAlign. Mol. Biol. Evol. (2015). doi:10.1093/molbev/msv029

    Google Scholar 

  14. Benzaid, B., El-Mabrouk, N.: Gene order alignment on trees with multiOrthoAlign. BMC-Genomics 15(Suppl. 6), S5 (2014)

    Article  Google Scholar 

  15. Benzaid, B., Dondi, R., El-Mabrouk, N.: Duplication-loss genome alignment: complexity and algorithm. In: Dediu, A.-H., Martín-Vide, C., Truthe, B. (eds.) LATA 2013. LNCS, vol. 7810, pp. 116–127. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  16. Holland, J.H.: Adaptation in natural and artificial systems. Ph.D. dissertation, University of Michigan (1975)

    Google Scholar 

  17. http://patricbrc.vbi.vt.edu/

  18. http://www.ncbi.nlm.nih.gov/

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Acknowledgments

The authors are grateful to anonymous referees for their helpful comments. This research is supported by the National Natural Science Foundation of China under Grant No. 61363035 and No. 61502111, Guangxi Natural Science Foundation under Grant No. 2015GXNSFAA139288, No. 2013GXNSFBA019263 and No. 2012GXNSFAA053219, Research Fund of Guangxi Key Lab of Multisource Information Mining and Security No. 14-A-03-02 and No. 15-A-03-02, “Bagui Scholar” Project Special Funds, Guangxi Collaborative Innovation Center of Multi-source Information Integration and Intelligent Processing.

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Authors and Affiliations

  1. Guangxi Key Lab of Multi-source Information Mining and Security, Guangxi Normal University, Guilin, 541004, China

    Jingli Wu

  2. College of Computer Science and Information Technology, Guangxi Normal University, Guilin, 541004, China

    Jingli Wu & Junwei Wang

Authors
  1. Jingli Wu
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  2. Junwei Wang
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Correspondence to Jingli Wu .

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Editors and Affiliations

  1. Tongji University , Shanghai, China

    De-Shuang Huang

  2. Polytechnic of Bari , Bari, Italy

    Vitoantonio Bevilacqua

  3. University of Wollongong , North Wollongong, New South Wales, Australia

    Prashan Premaratne

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Wu, J., Wang, J. (2016). A Practical Algorithm for the 2-Species Duplication-Loss Small Phylogeny Problem. In: Huang, DS., Bevilacqua, V., Premaratne, P. (eds) Intelligent Computing Theories and Application. ICIC 2016. Lecture Notes in Computer Science(), vol 9771. Springer, Cham. https://doi.org/10.1007/978-3-319-42291-6_33

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  • DOI: https://doi.org/10.1007/978-3-319-42291-6_33

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-42290-9

  • Online ISBN: 978-3-319-42291-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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