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Viral Genome Compression

  • Lucian Ilie
  • Liviu Tinta
  • Cristian Popescu
  • Kathleen A. Hill
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)

Abstract

Viruses compress their genome to reduce space. One of the main techniques is overlapping genes. We model this process by the shortest common superstring problem, that is, we look for the shortest genome which still contains all genes. We give an algorithm for computing optimal solutions which is slow in the number of strings but fast (linear) in their total length. This algorithm is used for a number of viruses with relatively few genes. When the number of genes is larger, we compute approximate solutions using the greedy algorithm which gives an upper bound for the optimal solution. We give also a lower bound for the shortest common superstring problem. The results obtained are then compared with what happens in nature. Remarkably, the compression obtained by viruses is quite high and also very close to the one achieved by modern computers.

Keywords

viruses viral genomes genome compression overlapping genes shortest common superstring problem exact algorithms approximate solutions lower bounds 

References

  1. 1.
    Armen, C., Stein, C.: Improved length bounds for the shortest superstring problem. In: Proc. 5th Internat. Workshop on Algorithms and Data Structures 1995. LNCS, vol. 955, pp. 494–505. Springer, Berlin (1995)Google Scholar
  2. 2.
    Armen, C., Stein, C.: A \(2\frac{2}{3}\) approximation algorithm for the shortest superstring problem. In: Hirschberg, D.S., Meyers, G. (eds.) CPM 1996. LNCS, vol. 1075, pp. 87–101. Springer, Heidelberg (1996)Google Scholar
  3. 3.
    Blum, A., Jiang, T., Li, M., Tromp, J., Yannakakis, M.: Linear approximation of shortest superstrings. J. Assoc. Comput. Mach. 41(4), 630–647 (1994)zbMATHMathSciNetGoogle Scholar
  4. 4.
    Breslauer, D., Jiang, T., Jiang, Z.: Rotations of periodic strings and short superstrings. J. Algorithms 24, 340–353 (1997)zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Cann, A.J.: Principles of Molecular Virology, 3rd edn. Elsevier Academic Press, London, San Diego (2001)Google Scholar
  6. 6.
    Chen, X., Li, M., Ma, B., Tromp, J.: DNACompress: fast and effective DNA sequence compression. Bioinformatics 18, 1696–1698 (2002)CrossRefGoogle Scholar
  7. 7.
    Crochemore, M., Rytter, W.: Jewels of Stringology. World Scientific Publisher, Singapore (2003)zbMATHGoogle Scholar
  8. 8.
    Czumaj, A., Gasieniec, L., Piotrow, M., Rytter, W.: Parallel and sequential approximations of shortest superstrings. In: Proc. First Scandinavian Workshop on Algorithm Theory. LNCS, vol. 824, pp. 95–106. Springer, Berlin (1994)Google Scholar
  9. 9.
    Daley, M., McQuillan, I.: Viral Gene Compression: Complexity and Verification. In: Domaratzki, M., Okhotin, A., Salomaa, K., Yu, S. (eds.) CIAA 2004. LNCS, vol. 3317, pp. 102–112. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  10. 10.
    Gallant, J., Maier, D., Storer, J.: On finding minimal length superstrings. Journal of Comput. and Syst. Sci. 20(1), 50–58 (1980)zbMATHCrossRefMathSciNetGoogle Scholar
  11. 11.
    Kosaraju, R., Park, J., Stein, C.: Long tours and short superstrings. In: Proc. 35th Annual IEEE Symposium on Foundations of Computer Science, pp. 166–177. IEEE Computer Society Press, Los Alamitos (1994)CrossRefGoogle Scholar
  12. 12.
    Krakauer, D.C.: Evolutionary principles of genomic compression. Comments on Theor. Biol. 7, 215–236 (2002)CrossRefGoogle Scholar
  13. 13.
    Lesk, A.: Introduction to Bioinformatics. Oxford University Press, Oxford (2002)Google Scholar
  14. 14.
    Lothaire, M.: Algebraic Combinatorics on Words. Cambridge University Press, Cambridge (2002)zbMATHGoogle Scholar
  15. 15.
    Storer, J.: Data Compression: Methods and Theory. Computer Science Press (1988)Google Scholar
  16. 16.
    Sweedyk, Z.: A \(2\frac{1}{2}\)-approximation algorithms for shortest superstring. SIAM J. Comput. 29(3), 954–986 (1999)CrossRefMathSciNetGoogle Scholar
  17. 17.
    Teng, S., Yao, F.: Approximating shortest superstrings. In: Proc. 34th Annual IEEE Symposium on Foundations of Computer Science, pp. 158–165. IEEE Computer Society Press, Los Alamitos (1993)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Lucian Ilie
    • 1
  • Liviu Tinta
    • 1
  • Cristian Popescu
    • 1
  • Kathleen A. Hill
    • 2
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondon, OntarioCanada
  2. 2.Department of BiologyUniversity of Western OntarioLondon, OntarioCanada

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