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Comput Appl Biosci. 1995 Feb;11(1):59-70.

Finding flexible patterns in a text: an application to three-dimensional molecular matching.

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Atelier de BioInformatique, CPASO-URA CNRS 448, Section de Physique et Chimie de l'Institut Curie, Paris, France.


Finding certain regularities in a text is an important problem in many areas, e.g. in the analysis of biological molecules such as nucleic acids or proteins. In the latter case, the text may be sequences of amino acids or a linear coding of three-dimensional structures, and the regularities then correspond to lexical or structural motifs common to two, or more, proteins. We first recall an earlier algorithm that found these regularities in a flexible way. Then we introduce a generalized version of this algorithm designed for the particular case of protein three-dimensional structures, since these structures present a few peculiarities that make them computationally harder to process. Finally, we give some applications of our new algorithm on concrete examples.

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