An Improved Algorithm for Generalized Comparison of Minisatellites
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One of the most important objects in genetic mapping and forensic studies are minisatellites. They consist of a heterogeneous tandem array of short repeat units called variants. The evolution of minisatellites is realized by tandem duplication and tandem deletion of variants. Jeffrey et al. proposed a method to obtain the sequence of variants, called maps. Bérard and Rivals designed the first algorithm of comparison of two minisatellite maps under an evolutionary model including deletion, insertion, mutation, amplification and contraction. The complexity of this first algorithm was O(n 4) in time and O(n 3) in space where n is the size of the maps. In this paper we propose a more efficient algorithm using the same evolutionary model which is O(n 3) in time and O(n 2) in space. Our algorithm with this better efficiency can even solve generalized and more refined models.
KeywordsEdit Distance Generalize Comparison Improve Algorithm Tree Representation Transformation Sequence
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- 1.Bérard, S., Rivals, E.: Comparison of Minisatellites. Proceedings of the 6th Annual International Conference on Research in Computational Molecular Biology. ACM Press, (2002).Google Scholar
- 6.Elemento, O., Gascuel, O., Lefranc, M.-P.: Reconstructing the duplication history of tandemly repeated genes. Molecular Biology and Evolution,vol 19(3). (2002) 278–288Google Scholar
- 7.Sankoff, D. and Kruskal, J.B: Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley. (1983)Google Scholar
- 8.Crochemore, M., Landau, G. M., Ziv-Ukelson, M.: A sub-quadratic sequence alignment algorithm for unrestricted cost matrices. SODA’2002. ACM-SIAM. (2002)679–688.Google Scholar