Computation of Repetitions and Regularities of Biologically Weighted Sequences
Manolis Christodoulakis, Costas S. Iliopoulos, Laurent Mouchard, Katerina Perdikuri, Athanasios Tsakalidis, Kostas Tsichlas · Journal of Computational Biology · 2006
Biological weighted sequences are used extensively in molecular biology as profiles for protein families, in the representation of binding sites and often for the representation of sequences produced by a shotgun sequencing strategy. In this paper, we address three fundamental problems in the area of biologically weighted sequences: (i) computation of repetitions, (ii) pattern matching, and (iii) computation of regularities. Our algorithms can be used as basic building blocks for more sophisticated algorithms applied on weighted sequences.