title: Computation of repetitions and regularities of biologically weighted sequences.
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.
authors.affiliation: Department of Computer Science, King's College London, London, United Kingdom.
authors.forename: M
authors.initials: M
authors.lastname: Christodoulakis
authors.forename: C
authors.initials: C
authors.lastname: Iliopoulos
authors.forename: L
authors.initials: L
authors.lastname: Mouchard
authors.forename: K
authors.initials: K
authors.lastname: Perdikuri
authors.forename: A
authors.initials: A
authors.lastname: Tsakalidis
authors.forename: K
authors.initials: K
authors.lastname: Tsichlas
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology; D006454:Hemoglobins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment
chemical_list: D006454:Hemoglobins