Searching for flexible repeated patterns using a non-transitive similarity relation
Pattern Recognition Letters
IJCAI '99 Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence
CPM '97 Proceedings of the 8th Annual Symposium on Combinatorial Pattern Matching
Fast and Sensitive Alignment of Large Genomic Sequences
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Rapid identification of repeated patterns in strings, trees and arrays
STOC '72 Proceedings of the fourth annual ACM symposium on Theory of computing
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The main goal of this paper is to present a new extension of KMRCRelat algorithm allowing Word Train searches. First, we recall the fundamental lemma of our KMRCRelat algorithm and we focus on the concept of flexible relational repeated words. Then, we introduce the concept of Word Trains and we show, in deep, the needed modification and extension to include such features in this algorithm. To illustrate Word Train searches, we present all details about KMRCRelat extension computation steps. We also show how this new extension is applicable to the characterization of short tandem repeat in DNA sequence providing an alternative way to solve originally this known problem in sequence analysis. Before concluding by introducing other possible KMRCRelat applications, the paper expands a set of experimental results obtained when applied to locus identification problem.