Affiliations: Department of Computer Science, King's
College London, Strand, London WC2R2LS, England. E-mail: csi@dcs.kcl.ac.uk | Department of Computer Engineering and Informatics,
University of Patras, 26504 Patras, Greece. E-mail: {makri,panagis,perdikur,
theodori}@ceid.upatras.gr | Research Academic Computer Technology Institute, N.
Kazantzaki Str., Rio 26504 Patras, Greece. E-mail: tsak@cti.gr
Abstract: In this paper we introduce the Weighted Suffix Tree, an efficient
data structure for computing string regularities in weighted sequences of
molecular data. Molecular Weighted Sequences can model important biological
processes such as the DNA Assembly Process or the DNA-Protein Binding Process.
Thus pattern matching or identification of repeated patterns, in biological
weighted sequences is a very important procedure in the translation of gene
expression and regulation. We present time and space efficient algorithms for
constructing the weighted suffix tree and some applications of the proposed
data structure to problems taken from the Molecular Biology area such as
pattern matching, repeats discovery, discovery of the longest common
subsequence of two weighted sequences and computation of covers.
