Introduction to algorithms
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Many algorithms have been proposed to date for the problemof finding biologically significant motifs in promoter regions. They can beclassified into two large families: combinatorial methods and probabilisticmethods. Probabilistic methods have been used more extensively, sincetheir output is easier to interpret. Combinatorial methods have the potentialto identify hard to detect motifs, but their output is much harderto interpret, since it may consist of hundreds or thousands of motifs.In this work, we propose a method that processes the output of combinatorialmotif finders in order to find groups of motifs that representvariations of the same motif, thus reducing the output to a manageablesize. This processing is done by building a graph that represents the cooccurrencesof motifs, and finding communities in this graph. We showthat this innovative approach leads to a method that is as easy to useas a probabilistic motif finder, and as sensitive to low quorum motifsas a combinatorial motif finder. The method was integrated with twocombinatorial motif finders, and made available on the Web.