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
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
T.F. Smith, M.S. Waterman: J. Mol. Biol. 147, 195 (1981)
R. Hughey, A. Krogh: CABIOS 12, 95 (1996)
A. Dembo, S. Karlin, O. Zeitouni: Ann. Prob. 22, 2022 (1994)
S. Karlin, S.F. Altschul: Proc. Natl. Acad. Sci. USA 87, 2264 (1990)
E.J. Gumbel: Statistics of Extremes (Columbia University Press, New York 1958 )
S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman: J. Mol. Biol. 215, 403 (1990)
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.
S. Henikoff, J.G. Henikoff: Proc. Natl. Acad. Sci. USA 89, 10915 (1992)
S.B. Needleman, C.D. Wunsch: J. Mol. Biol. 48, 433 (1970)
Y.-K. Yu, T. Hwa: J. Comp. Biol. 8, 249 (2001)
R. Arratia, P. Morris, M.S. Waterman: J. Appl. Probab. 25, 106 (1988)
S. Karlin, S.F Altschul: Proc. Natl. Acad. Sci. USA 90, 5873 (1993)
S. Karlin, A. Dembo: Adv. Appl. Prob. 24, 113 (1992)
M.S. Waterman, L. Gordon, R. Arratia: Proc. Natl. Acad. Sci. U.S.A. 84, 1239 (1987)
R. Arratia, M.S. Waterman: Ann. Appl. Prob. 4, 200 (1994)
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
T.F. Smith, M.S. Waterman, C. Burks: Nucleic Acids Research 13, 645 (1985)
J.F. Collins, A.F.W. Coulson, A. Lyall: CABIOS 4, 67 (1988)
R. Mott: Bull. Math. Biol. 54, 59 (1992)
M.S. Waterman, M. Vingron: Stat. Sci. 9, 367 (1994)
M.S. Waterman, M. Vingron: Proc. Natl. Acad. Sci. USA 91, 4625 (1994)
S.F. Altschul, W. Gish: Methods in Enzymology 266, 460 (1996)
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
S. Eddy, G. Mitchison, R.Durbin: J. Comp. Biol. 2, 9 (1995)
A. Milosavljevic, J. Jurka: CABIOS 9, 407 (1993)
C. Barret, R. Hughey, K. Karplus: CABIOS 13, 191 (1997)
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
R. Mott, R. Tribe: J. Comp. Biol. 6, 91 (1999)
D. Siegmund, B. Yakir: Ann. Stat. 28, 657 (2000)
D.S. Fisher, D.A. Huse: Phys. Rev. B 43, 10728 (1991)
T. Halpin-Healy, Y.-C. Zhang: Phys. Rep. 254, 215 (1995)
Y.-K. Yu, R. Bundschuh, T. Hwa: Bioinformatics 18, 865 (2002)
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
A.G. Murzin, S.E. Brenner, T. Hubbard, C. Chothia: J. Mol. Biol. 47, 536 (1995)
S.E. Brenner, C. Chothia, T.J.P. Hubbard: Proc. Natl. Acad. Sci. USA 95, 6073 (1998)
M. Gribskov, N.L. Robinson: Comput. Chem. 20, 25 (1996)
M.J. Bishop, E.A. Thompson: J. Mol. Biol. 190, 159 (1986)
Rigorously speaking, the weight W [a, b] is given by
J.L. Thorne, H. Kishino, J. Felsenstein: J. Mol. Evol. 33, 114 (1991)
J.L. Thorne, H. Kishino, J. Felsenstein: J. Mol. Evol. 34, 3 (1992)
Editor information
Editors and Affiliations
Rights 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