ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation

Authors:
C. Di Pietro;V. Di Pietro;G. Emmanuele;A. Ferro;T. Maugeri;E. Modica;G. Pigola;A. Pulvirenti;M. Purrello;M. Ragusa;M. Scalia;D. Shasha;S. Travali;V. Zimmitti
Affiliations:
-;-;-;-;-;-;-;-;-;-;-;-;-;-
Venue:
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Year:
2003

Citing 4
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Abstract

In this paper we present a new Multiple SequenceAlignment (MSA) algorithm called AntiClusAl.Themethod makes use of the commonly use idea ofaligning homologous sequences belonging to classesgenerated by some clustering algorithm, and thencontinue the alignment process ina bottom-up wayalong a suitable tree structure.The final result isthen read at the root of the tree.Multiple sequencealignment in each cluster makes use of the progressivealignment with the 1-median (center) of the cluster.The 1-median of set S of sequences is the elementof S which minimizes the average distance from anyother sequence in S.Its exact computation requiresquadratic time.The basic idea of our proposedalgorithm is to make use of a simple and natural algorithmictechnique based on randomized tournamentswhich has been successfully applied to large size searchproblems in general metric spaces.In particular aclustering algorithm called Antipole tree and an approximatelinear 1-median computation are used.Ouralgorithm compared with Clustal W, a widely used toolto MSA, shows a better running time results with fullycomparable alignment quality.A successful biologicalapplication showing high aminoacid conservationduring evolution of Xenopus laevis SOD2 is also cited.