Abstract
This paper provides a novel approach to improve the Needleman-Wunsch algorithm, one of the most basic algorithms in Protein or DNA sequence pairwise alignment. In the first part, the problem of this algorithm is outlined. Later, a general introduction of related work is described. Finally, a modified Needleman-Wunsch algorithm and experimental results are presented. The importance of this process lies on its effect of keeping common patterns in sequences to be aligned accurately.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981)
Smith, T.F., Waterman, M.S.: Comparison of biosequences. Adv. Appl. Math. 2 (1981)
Henikoff, S., Henikoff, J.G., Pietrokovski, S.: Blocks+: A non-redundant database of protein alignment blocks dervied from multiple compilations. Bioinformatics 15(6), 471–479 (1999)
Henikoff, J.G., Greene, E.A., Pietrokovski, S., Henikoff, S.: Increased coverage of protein families with the blocks database servers. Nucleic Acids. Res. 28, 228–230 (2000)
Comet, J.-P., Henry, J.: Pairwise sequence alignment using a PROSITE patternderived similarity score. Computers and Chemistry 26, 421–436 (2002)
Su, Q., Lu, L., Brutlab, D.: eBlocks (2002), http://fold.stanford.edu/eblocks
Altschul, S.F., Madden, T.L., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Henikoff, S., Henikoff, J.G.: The prosite database. Nucleic Acids Res. 19(23), 6565–6572 (1999)
Hofmann, K., Bucher, P., Falquet, L., Bairoch, A.: Automated assembly of protein blocks for database searching. Nucleic Acids Res. 27, 215–219 (1991)
Dayhoff, M.O.: Survey of new data and computer methods of analysis. In: Atlas of protein sequence and structure. National Biomedical Research Foundation, vol. 5(Suppl. 3), Georgetown University, Washington (1978)
Henikoff, S., Henikoff, J.G.: Amino acid substitution matrics from protein blocks. Proc. Natl. Acad. Sci. 89, 10915–10919 (1992)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Du, Z., Lin, F. (2004). Improvement of the Needleman-Wunsch Algorithm. In: Tsumoto, S., Słowiński, R., Komorowski, J., Grzymała-Busse, J.W. (eds) Rough Sets and Current Trends in Computing. RSCTC 2004. Lecture Notes in Computer Science(), vol 3066. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-25929-9_101
Download citation
DOI: https://doi.org/10.1007/978-3-540-25929-9_101
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22117-3
Online ISBN: 978-3-540-25929-9
eBook Packages: Springer Book Archive