Skip to main content
Springer Nature Link
Log in

A Local Chaining Algorithm and Its Applications in Comparative Genomics

  • Conference paper
Algorithms in Bioinformatics (WABI 2003)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2812))

Included in the following conference series:

Abstract

Given fragments from multiple genomes, we will show how to find an optimal local chain of colinear non-overlapping fragments in sub-quadratic time, using methods from computational geometry. A variant of the algorithm finds all significant local chains of colinear non-overlapping fragments. The local chaining algorithm can be used in a variety of problems in comparative genomics: The identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements such as transpositions and inversions, and exon prediction.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

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.

Similar content being viewed by others

References

  1. Abouelhoda, M.I., Ohlebusch, E.: Multiple genome alignment: Chaining algorithms revisited. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 1–16. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  2. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: The enhanced suffix array and its applications to genome analysis. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 449–463. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: A basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)

    Google Scholar 

  4. Batzoglou, S., Pachter, L., Mesirov, J.P., Berger, B., Lander, E.S.: Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Research 10, 950–958 (2001)

    Article  Google Scholar 

  5. Bently, J.L.: K-d trees for semidynamic point sets. In: 6th Annual ACM Symposium on Computational Geometry, pp. 187–197. ACM, New York (1990)

    Chapter  Google Scholar 

  6. Blattner, F.R., et al.: The complete genome sequence of Escherichia coli K-12. Science 277(5331), 1453–1474 (1997)

    Article  Google Scholar 

  7. Bray, N., Dubchak, I., Pachter, L.: AVID: A global alignment program. Genome Research 13, 97–102 (2003)

    Article  Google Scholar 

  8. Brudno, M., Morgenstern, B.: Fast and sensitive alignment of large genomic sequences. In: Proceedings of the IEEE Computer Society Bioinformatics Conference, pp. 138–150. IEEE, Los Alamitos (2002)

    Chapter  Google Scholar 

  9. Chain, P., Kurtz, S., Ohlebusch, E., Slezak, T.: An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges. Briefings in Bioinformatics 4(2) (2003)

    Google Scholar 

  10. Chazelle, B.: A functional approach to data structures and its use in multidimensional searching. SIAM Journal on Computing 17(3), 427–462 (1988)

    Article  MATH  MathSciNet  Google Scholar 

  11. Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., Salzberg, S.L.: Alignment of whole genomes. Nucleic Acids Res. 27, 2369–2376 (1999)

    Article  Google Scholar 

  12. Delcher, A.L., Phillippy, A., Carlton, J., Salzberg, S.L.: Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30(11), 2478–2483 (2002)

    Article  Google Scholar 

  13. Eisen, J.A., Heidelberg, J.F., White, O., Salzberg, S.L.: Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1(6), 1–9 (2000)

    Article  Google Scholar 

  14. Eppstein, D.: http://www.ics.uci.edu/eppstein/pubs/p-sparsedp.html

  15. Eppstein, D., Giancarlo, R., Galil, Z., Italiano, G.F.: Sparse dynamic programming. I:Linear cost functions; II:Convex and concave cost functions. Journal of the ACM 39, 519–567 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  16. Heidelberg, J.F., et al.: DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483 (2000)

    Article  Google Scholar 

  17. Himmelreich, R., Plagens, H., Hilbert, H., Reiner, B., Herrmann, R.: Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25, 701–712 (1997)

    Article  Google Scholar 

  18. Hughes, D.: Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes. Genome Biology 1(6), reviews 0006.1–0006.8 (2000)

    Google Scholar 

  19. Johnson, D.B.: A priority queue in which initialization and queue operations take O(log logD) time. Math. Sys. Theory 15, 295–309 (1982)

    Article  MATH  Google Scholar 

  20. Kent, W.J., Zahler, A.M.: Conservation, regulation, synteny, and introns in a large-scale C.briggsae-C.elegans genomic alignment. Genome Research 10, 1115–1125 (2000)

    Article  Google Scholar 

  21. Lee, D.T., Wong, C.K.: Worst-case analysis for region and partial region searches in multidimensional binary search trees and balanced quad trees. Acta Informatica 9, 23–29 (1977)

    Article  MATH  MathSciNet  Google Scholar 

  22. Höhl, M., Kurtz, S., Ohlebusch, E.: Efficient multiple genome alignment. In: Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology. Bioinformatics, vol. 18(Suppl. 1), pp. 312–320 (2002)

    Google Scholar 

  23. Morgenstern, B.: A space-efficient algorithm for aligning large genomic sequences. Bioinformatics 16, 948–949 (2000)

    Article  Google Scholar 

  24. Myers, E.W., Miller, W.: Chaining multiple-alignment fragments in subquadratic time. In: Proceedings of the 6th ACM-SIAM Symposium on Discrete Algorithms, pp. 38–47 (1995)

    Google Scholar 

  25. Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444–2448 (1988)

    Article  Google Scholar 

  26. Preparata, F.P., Shamos, M.I.: Computational geometry: An introduction. Springer, New York (1985)

    Google Scholar 

  27. Roytberg, M.A., Ogurtsov, A.Y., Shabalina, S.A., Kondrashov, A.S.: A hierarchical approach to aligning collinear regions of genomes. Bioinformatics 18, 1673–1680 (2002)

    Article  Google Scholar 

  28. Schwartz, S., Kent, J.K., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., Miller, W.: Human-mouse alignments with BLASTZ. Genome Research 13, 103–107 (2003)

    Article  Google Scholar 

  29. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., Miller, W.: PipMaker—A web server for aligning two genomic DNA sequences. Genome Research 10(4), 577–586 (2000)

    Article  Google Scholar 

  30. van Emde Boas, P.: Preserving order in a forest in less than logarithmic time and linear space. Information Processing Letters 6(3), 80–82 (1977)

    Article  MATH  Google Scholar 

  31. Vincens, P., Buffat, L., Andre, C., Chevrolat, J.P., Boisvieux, J.F., Hazout, S.: A strategy for finding regions of similarity in complete genome sequences. Bioinformatics 14, 715–725 (1998)

    Article  Google Scholar 

  32. Zhang, Z., Raghavachari, B., Hardison, R.C., Miller, W.: Chaining multiplealignment blocks. J. Computational Biology 1, 51–64 (1994)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Technology, University of Bielefeld, P.O. Box 10 01 31, 33501, Bielefeld, Germany

    Mohamed Ibrahim Abouelhoda

  2. Faculty of Computer Science, University of Ulm, 89069, Ulm, Germany

    Enno Ohlebusch

Authors
  1. Mohamed Ibrahim Abouelhoda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Enno Ohlebusch
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, 10029-6574, New York, NY

    Gary Benson

  2. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow, G12 8QQ, Glasgow, Scotland

    Roderic D. M. Page

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Abouelhoda, M.I., Ohlebusch, E. (2003). A Local Chaining Algorithm and Its Applications in Comparative Genomics. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-39763-2_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20076-5

  • Online ISBN: 978-3-540-39763-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics