Abstract
In this paper we present a more efficient algorithm for comparison of minisatellites which has complexity O(n’3+ m’3 + mn’2+ nm’2 +mn) where n and m are the lengths of the maps and n’ and m’ are the sizes of run-length encoded maps. We show that this algorithm makes a significant improvement for the real biological data, dividing the computing time by a factor 30 on a significant set of data.
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
Apostolico, A., Landau, G.M., Skiena, S.: Matching for Run Length Encoded Strings. Journal of Complexity 15(1), 4–16 (1999)
Arbell, O., Landau, G.M., Mitchell, J.S.B.: Edit Distance of Run-Length Encoded Strings. Information Processing Letter 83(6), 307–314 (2002)
Bunke, H., Csirik, J.: An Improved Algorithm for Computing the Edit Distance of Run Length Coded Strings. Information Processing Letters 54, 93–96 (1995)
Behzadi, B., Steyaert, J.-M.: An Improved Algorithm for Generalized Comparison of Minisatellites. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 32–41. Springer, Heidelberg (2003)
Mäkinen, V., Navarro, G., Ukkonen, E.: Approximate Matching of Run-Length Compressed Strings. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 31–49. Springer, Heidelberg (2001)
Bérard, S., Rivals, E.: Comparison of Minisatellites. In: Proceedings of the 6th Annual International Conference on Research in Computational Molecular Biology, ACM Press, New York (2002)
Jobling, M.A., Bouzekri, N., Taylor, P.G.: Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1(DYF155S1). Human Molecular Genetics 7(4), 643–653 (1998)
Bouzekri, N., Taylor, P.G., Hammer, M.F., Jobling, M.A.: Novel mutation processes in the evolution of haploid minisatellites, MSY1: array homogenization without homogenization. Human Molecular Genetics 7(4), 655–659 (1998)
Jeffreys, A.J., Tamaki, K., Macleod, A., Monckton, D.G., Neil, D.L., Armour, J.A.L.: Complex gene conversion events in germline mutation at human minisatellites. Nature Genetics 6, 136–145 (1994)
Brión, M., Cao, R., Salas, A., Lareu, M.V., Carracedo, A.: New Method to Measure Minisatellite Variant Repeat Variation in Population Genetic Studies. American Journal of Human Biology 14, 421–428 (2002)
Elemento, O., Gascuel, O., Lefranc, M.-P.: Reconstructing the duplication history of tandemly repeated genes. Molecular Biology and Evolution 19(3), 278–288 (2002)
Sankoff, D., Kruskal, J.B.: Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading (1983)
Crochemore, M., Landau, G.M., Ziv-Ukelson, M.: A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. In: SODA 2002, pp. 679–688. ACM-SIAM (2002)
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
Behzadi, B., Steyaert, JM. (2004). The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach. In: Jonassen, I., Kim, J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science(), vol 3240. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30219-3_25
Download citation
DOI: https://doi.org/10.1007/978-3-540-30219-3_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-23018-2
Online ISBN: 978-3-540-30219-3
eBook Packages: Springer Book Archive