Abstract
An important goal in sequence analysis is to identify features in sequence alignments that are reflections of the evolutionary history of the sequences rather than artifacts of the alignment method. We have developed a new measure for determining a distance between sequence alignments that will assist us in reaching this goal. We apply this new measure to alignments produced by three different sequence alignment programs and an alignment created by structural superposition.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abola, E.W., Bernstein, F.C., Bryant, S., Koetzle, T.F., Weng, T., 1987, in Crystallographic Databases–Information Content, Software Systems, Scientific Applications, eds., Allen, F.H., Bergerhoff, G., Sievers, R. Data Comission of the International Union of Crystallography, Bonn, Cambridge, Chester, pp 107–132.
Altschul, S.F., 1989. Gap Costs for Multiple Sequence Alignment. J. Theor. Biol. 138: 297–309.
Altschul, S.F., Lipman, D.J., 1989. Trees, stars, and multiple biological sequence alignment. SIAM J. Appl. Math. 49: 197–209.
Bairoch, A., Boeckmann, B., 1993. The Swiss-PROT protein sequence data bank, recent developments. Nuc. Acids. Res. 21: 3093–3096.
Barton, G., 1990, Protein multiple sequence alignment and flexible pattern matching, Methods in Enzymology. 183: 403–428.
Barton, G., Sternberg, M., 1987, Evaluation and improvements in the automatic alignment of protein sequences, Protein Engineering. 1: 89–94.
Clark, S.P., 1992, Maligned: a multiple sequence alignment editor, CABIOS. 8: 535–538.
Dayhoff, M., Schwartz, R., Orcutt, B., 1978, A model for evolutionary change in proteins, Atlas of Protein Sequence and Structure. 5: 3: 345–352.
Feng, D., Doolittle, R. 1990, Progressive alignment and phylogenetic tree construction of protein sequences, Methods in Enzymology. 183: 403–428.
Genetics Computer Group, 1991, Program Manual for the GCG Package, Version 7.
Kruskal, J.B., 1983, An overview of sequence comparision I, Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. 1–44.
Lipman, D.J., Altschul, S.F., and Kececioglu, J.D., 1989, A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA. 86: 4412–4415.
Pascarella, S., Argos, P., 1992, A data bank merging related protein structures and sequences Protein. Engineering. 5: 121–137.
Smith, T.F., Waterman, M.S., Fitch, W.M. 1981, Comparative biosequence metrics, J. Mol. Evol. 18: 38–46
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1995 Springer Science+Business Media New York
About this chapter
Cite this chapter
Nicholas, H.B., Ropelewski, A.J., Deerfield, D.W., Behrmann, J.G. (1995). A Metric Measure for Comparing Sequence Alignments. In: Atassi, M.Z., Appella, E. (eds) Methods in Protein Structure Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1031-8_47
Download citation
DOI: https://doi.org/10.1007/978-1-4899-1031-8_47
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-1033-2
Online ISBN: 978-1-4899-1031-8
eBook Packages: Springer Book Archive