Structured motifs search

Authors:
Alberto Policriti;Nicola Vitacolonna;Michele Morgante;Andrea Zuccolo
Affiliations:
Department of Mathematics and Computer Science, Udine, Italy;Department of Mathematics and Computer Science, Udine, Italy;Department of Crop Sciences and Agricultural Engineering, Udine, Italy;Department of Crop Sciences and Agricultural Engineering, Udine, Italy
Venue:
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Year:
2004

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Abstract

In this paper we describe an algorithm for the localization of structured models, i.e. sequences of (simple) motifs and distance constraints. It basically combines standard pattern matching procedures with a constraint satisfaction solver, and it has the ability, not present in similar tools, to search for partial matches. A significant feature of our approach, especially in terms of efficiency for the application context, is that the (potentially) exponentially many solutions to the considered problem are represented in compact form as a graph. Moreover, the time and space necessary to build the graph are linear in the number of occurrences of the component patterns.