PRATT paper in Protein Science

Finding flexible patterns in unaligned protein sequences.
Inge Jonassen, John F. Collins, Desmond Higgins
Protein Science 1995;4(8):1587-1595
Communication to:
Inge Jonassen,
Department of Informatics,
University of Bergen
N5020 Bergen

flexible gaps, patterns, protein families, PROSITE.
We present a new method for the identification of conserved patterns in a set of unaligned related protein sequences. It is able to discover patterns of a quite general form, allowing for both ambiguous positions and for variable length wildcard regions. It allows the user to define a class of patterns (e.g., the degree of ambiguity allowed and the length and number of gaps), and the method is then guaranteed to find the conserved patterns in this class scoring highest according to a significance measure defined. Identified patterns may be refined using one of two new algorithms. We present a new (nonstatistical) significance measure for flexible patterns. The method is shown to recover known motifs for PROSITE families and is also applied to some recently described families from the literature.

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