Skip to main content

Sequence Alignment in Bioinformatics

  • Chapter
  • 630 Accesses

Abstract

Over two billion US dollars have been budgeted for the Human Genome Project alone in the past twelve years, not to mention other similar or related projects worldwide. These investments have led to the production of enormous amount of biological data, many of which are sequence information of biomolecules — e.g. specifying proteins/DNAs by identifying each amino-acid/nucleotide in the sequential order. These sequence data, presumably containing the “digital” information of life, are hard to decipher. Extracting useful and important information out of those massive biological data has developed into a new branch of science — bioinformatics. One of the most important and widely used method in bioinformatics research is called “sequence alignment”. The basic idea is to expedite the identification of biological functions of a newly sequenced biomolecule, say a protein, by comparing the sequence content of the new molecule to the existing ones (characterized and documented in the database).

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

Buying options

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
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover 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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. T.F. Smith, M.S. Waterman: J. Mol. Biol. 147, 195 (1981)

    Article  Google Scholar 

  2. R. Hughey, A. Krogh: CABIOS 12, 95 (1996)

    Google Scholar 

  3. A. Dembo, S. Karlin, O. Zeitouni: Ann. Prob. 22, 2022 (1994)

    Article  MathSciNet  MATH  Google Scholar 

  4. S. Karlin, S.F. Altschul: Proc. Natl. Acad. Sci. USA 87, 2264 (1990)

    Article  ADS  MATH  Google Scholar 

  5. E.J. Gumbel: Statistics of Extremes (Columbia University Press, New York 1958 )

    Google Scholar 

  6. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman: J. Mol. Biol. 215, 403 (1990)

    Google Scholar 

  7. M.O. Dayhoff, R.M. Schwartz, B.C. Orcutt: `A Model of Evolutionary Change in Proteins’. In Atlas of Protein Sequence and Structure, Ed. by M.O. Dayhoff, R.V. Eck, 5 supp. 3, pp. 345–358 (1978), Natl. Biomed. Res. Found.

    Google Scholar 

  8. S. Henikoff, J.G. Henikoff: Proc. Natl. Acad. Sci. USA 89, 10915 (1992)

    Article  ADS  Google Scholar 

  9. S.B. Needleman, C.D. Wunsch: J. Mol. Biol. 48, 433 (1970)

    Article  Google Scholar 

  10. Y.-K. Yu, T. Hwa: J. Comp. Biol. 8, 249 (2001)

    Article  Google Scholar 

  11. R. Arratia, P. Morris, M.S. Waterman: J. Appl. Probab. 25, 106 (1988)

    Article  MathSciNet  MATH  Google Scholar 

  12. S. Karlin, S.F Altschul: Proc. Natl. Acad. Sci. USA 90, 5873 (1993)

    Article  ADS  Google Scholar 

  13. S. Karlin, A. Dembo: Adv. Appl. Prob. 24, 113 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  14. M.S. Waterman, L. Gordon, R. Arratia: Proc. Natl. Acad. Sci. U.S.A. 84, 1239 (1987)

    Article  MathSciNet  ADS  Google Scholar 

  15. R. Arratia, M.S. Waterman: Ann. Appl. Prob. 4, 200 (1994)

    Article  MathSciNet  MATH  Google Scholar 

  16. R. Bundschuh, T. Hwa: in RECOMB99 — Proceedings of the Third Annual International Conference on Computational Molecular Biology, Ed. by S. Istrail, P. Pevzner, M. Waterman, ( ACM Press, New York 1999 ) pp. 25–32

    Google Scholar 

  17. T.F. Smith, M.S. Waterman, C. Burks: Nucleic Acids Research 13, 645 (1985)

    Article  Google Scholar 

  18. J.F. Collins, A.F.W. Coulson, A. Lyall: CABIOS 4, 67 (1988)

    Google Scholar 

  19. R. Mott: Bull. Math. Biol. 54, 59 (1992)

    MATH  Google Scholar 

  20. M.S. Waterman, M. Vingron: Stat. Sci. 9, 367 (1994)

    Article  MathSciNet  MATH  Google Scholar 

  21. M.S. Waterman, M. Vingron: Proc. Natl. Acad. Sci. USA 91, 4625 (1994)

    Article  ADS  MATH  Google Scholar 

  22. S.F. Altschul, W. Gish: Methods in Enzymology 266, 460 (1996)

    Article  Google Scholar 

  23. R. Olsen, R. Bundschuh, T. Hwa: `Rapid Assessment of Extremal Statistics for Gapped Local Alignment’. in Proceedings of The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB99), Ed. by T. Lengauer ( AAAI Press, Menlo Park 1999 ) pp. 211–222

    Google Scholar 

  24. S. Eddy, G. Mitchison, R.Durbin: J. Comp. Biol. 2, 9 (1995)

    Article  Google Scholar 

  25. A. Milosavljevic, J. Jurka: CABIOS 9, 407 (1993)

    Google Scholar 

  26. C. Barret, R. Hughey, K. Karplus: CABIOS 13, 191 (1997)

    Google Scholar 

  27. R. Bundschuh: `An Analytic Approach to Significance Assessment in Local Sequence Alignment with Gaps’ in Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, Ed. by R. Shamir, S. Miyano, S. Istrail, P. Pevzner, M. Waterman ( ACM press, New York 2000 ) pp. 86–95

    Google Scholar 

  28. R. Mott, R. Tribe: J. Comp. Biol. 6, 91 (1999)

    Article  Google Scholar 

  29. D. Siegmund, B. Yakir: Ann. Stat. 28, 657 (2000)

    MathSciNet  MATH  Google Scholar 

  30. D.S. Fisher, D.A. Huse: Phys. Rev. B 43, 10728 (1991)

    Article  ADS  Google Scholar 

  31. T. Halpin-Healy, Y.-C. Zhang: Phys. Rep. 254, 215 (1995)

    Article  ADS  Google Scholar 

  32. Y.-K. Yu, R. Bundschuh, T. Hwa: Bioinformatics 18, 865 (2002)

    Google Scholar 

  33. Y.-k. Yu, R. Bundschuh, T. Hwa: `Statistical Significance and Extreme Ensemble of Gapped Local Hybrid Alignment’, in Biological Evolution and Statistical Physics (Lecture Notes in Physics, vol 585 ), Ed. by M. Lassig, A. Valleriani ( Springer Verlag, Berlin 2002 ) pp. 3–21

    Google Scholar 

  34. A.G. Murzin, S.E. Brenner, T. Hubbard, C. Chothia: J. Mol. Biol. 47, 536 (1995)

    Google Scholar 

  35. S.E. Brenner, C. Chothia, T.J.P. Hubbard: Proc. Natl. Acad. Sci. USA 95, 6073 (1998)

    Article  ADS  Google Scholar 

  36. M. Gribskov, N.L. Robinson: Comput. Chem. 20, 25 (1996)

    Article  Google Scholar 

  37. M.J. Bishop, E.A. Thompson: J. Mol. Biol. 190, 159 (1986)

    Article  Google Scholar 

  38. Rigorously speaking, the weight W [a, b] is given by

    Google Scholar 

  39. J.L. Thorne, H. Kishino, J. Felsenstein: J. Mol. Evol. 33, 114 (1991)

    Article  Google Scholar 

  40. J.L. Thorne, H. Kishino, J. Felsenstein: J. Mol. Evol. 34, 3 (1992)

    Article  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Yu, YK. (2004). Sequence Alignment in Bioinformatics. In: Wille, L.T. (eds) New Directions in Statistical Physics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-08968-2_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-08968-2_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-07739-5

  • Online ISBN: 978-3-662-08968-2

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics