Skip to main content
SpringerLink
Log in

A Novel Method for Progressive Multiple Sequence Alignment Based on Lempel-Ziv

  • Conference paper
Neural Information Processing (ICONIP 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5863))

Included in the following conference series:

Abstract

In this paper, we propose LZ_MSA, a novel method for progressive multiple sequence alignment based on Lempel-Ziv. The vector space is constructed by 10 types of copy modes. Under this approach, sequence alignment is converted into vector alignment and the guide tree can be dynamically amended. Finally we use five subsets in the standard dataset of BAliBASE to validate the proposed algorithm. Compared to ClusatalW, MAFFT, LZ_MSA reduces the alignment time without sacrificing accuracy.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Russell, D.J., Otu, H.H., Sayood, K.: Grammar-based distance in progressive multiple sequence alignment. In: BMC Bioinformatics (2008)

    Google Scholar 

  2. Notredame, C.: Recent Evolutions of Multiple Sequence Alignment Algorithms. PLoS Computational Biology 3(8), 1405–1408 (2007)

    Article  Google Scholar 

  3. Kim, J., Pramanik, S., Chung, M.J.: Multiple sequence alignment using simulated annealing. BMC Bioinformatics 10, 419–426 (1994)

    Google Scholar 

  4. Kim, J., Cole, J.R., Pramanik, S.: Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. BMC Bioinformatics 12, 259–267 (1996)

    Google Scholar 

  5. Anbarasu, L.A., Narayanasamy, P., Sundararajan, V.: Multiple Sequence Alignment using parallel genetic algorithm. In: The Second Asia Pacific Conference on Simulated Annealing, Canberra, Australia (1998)

    Google Scholar 

  6. Gonzalez, R.R., Izquierdo, C.M., Seijas, J.: Multiple Protein Sequence comparison by genetic algorithms. In: SP IE298 (1999)

    Google Scholar 

  7. Zhang, C., Wong, A.K.C.: A genetic algorithm for multiple molecular sequence alignment. BMC Bioinformatics 13, 565–581 (1997)

    Google Scholar 

  8. Notredame, C., Higgins, D.G.: SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research 24, 1515–1524 (1996)

    Article  Google Scholar 

  9. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTALW: improving the sensitivity of progressive multiple sequence alignent through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680 (1994)

    Article  Google Scholar 

  10. Gotoh, O.: Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments. Journal of Molecular Biology 264, 823–838 (1996)

    Article  Google Scholar 

  11. Katoh, K., Misawa, K., Kuma, K.-i., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30, 3059–3066 (2002)

    Article  Google Scholar 

  12. Lempel, A., Ziv, J.: On the complexity of finite sequences. IEEE Transactions on information theory 22(1) (1976)

    Google Scholar 

  13. Feng, D.F., Doolittle, R.F.: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Molecular Biology and Evolution 25(4), 351–360 (1987)

    Google Scholar 

  14. Gotoh, O.: Significant improvement in accuracy of multiple protein sequence alignment by iterative refinement as assessed by reference to structural alignment. Journal of Molecular Biology 264, 823–838 (1996)

    Article  Google Scholar 

  15. Zheng, X., Li, C., Wang, J.: A complexity-based measure and its application to phylogenetic analysis. Journal of Mathematical Chemistry 43, 26–31 (2008)

    Article  MathSciNet  Google Scholar 

  16. Fitch, W.M., Margoliash, E.: Construction of phylogenetic trees. Science 155, 279–284 (1967)

    Article  Google Scholar 

  17. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic tree. Molecular Biology and Evolution 4, 406–425 (1987)

    Google Scholar 

  18. Carrillo, H., Lipman, D.: The multiple sequence alignment problem in biology. SIAM Journal on Applied Mathematics 48(5), 1073–1082 (1988)

    Article  MATH  MathSciNet  Google Scholar 

  19. Thompson, J.D., Plewniak, F., Poch, O.: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Research 27(13), 2689–2690 (1999)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Automation, Xiamen University, 361005, Xiamen, China

    Guoli Ji, Congting Ye & Zhenya Guo

  2. School of Information Technology, York University, Toronto, Canada, M3J 1P3

    Zijiang Yang

Authors
  1. Guoli Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Congting Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zijiang Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhenya Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Electronic Engineering, City University of Hong Kong, Hong Kong,  

    Chi Sing Leung

  2. School of Electrical Engineering and Computer Science, Kyungpook National University, 1370 Sankyuk-Dong, Puk-Gu, 702-701, Taegu, Korea

    Minho Lee

  3. School of Information Technology, King Mongkut’s University of Technology Thonburi, 126 Pracha-U-Thit Rd., Bangmod, Thungkru, 10140, Bangkok, Thailand

    Jonathan H. Chan

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ji, G., Ye, C., Yang, Z., Guo, Z. (2009). A Novel Method for Progressive Multiple Sequence Alignment Based on Lempel-Ziv. In: Leung, C.S., Lee, M., Chan, J.H. (eds) Neural Information Processing. ICONIP 2009. Lecture Notes in Computer Science, vol 5863. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10677-4_17

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-10677-4_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-10676-7

  • Online ISBN: 978-3-642-10677-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation