Incremental Inference of Relational Motifs with a Degenerate Alphabet
In this paper we define a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of elements of the motifs. For this class of problems we give an algorithm that is a suitable extension of the KMR  paradigm and, in particular, of the KMRC  as it uses a degenerate alphabet. The algorithm contains several improvements with respect to  that result especially useful when – as it is required for relational motifs – the inference is made by partially overlapping shorter motifs. The efficiency, correctness and completeness of the algorithm is assured by several non-trivial properties. Finally, we list some possible applications and we focus on one of them: the study of 3D structures of proteins.
KeywordsInput Sequence Repeated Motif Input Size Repeated Pattern Input Text
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- 1.El-Zant, N., Soldano, H.: Finding repeated flexible relational words in sequences. Journal of Systemics, Cybernetics and Informatics 2(4) (2004)Google Scholar
- 2.Jones, N.C., Pevzner, P.A.: An Introduction to Bioinformatics Algorithms. The MIT Press, Cambridge (2004)Google Scholar
- 3.Karp, R., Miller, R., Rosenberg, A.: Rapid identification of repated patterns in strings, trees and arrays. In: Fourth ACM Symposium on Theory of Computing, pp. 125–136 (1972)Google Scholar