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Updated: Aug 6, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Computation of repetitions and regularities of biologically weighted sequences
M Christodoulakis1, C Iliopoulos, L Mouchard
1Department of Computer Science, King's College London, London, United Kingdom.
Abstract:
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.
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