Improved Filters for the Approximate Suffix-Prefix Overlap Problem
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- Kucherov G., Tsur D. (2014) Improved Filters for the Approximate Suffix-Prefix Overlap Problem. In: Moura E., Crochemore M. (eds) String Processing and Information Retrieval. SPIRE 2014. Lecture Notes in Computer Science, vol 8799. Springer, Cham
Computing suffix-prefix overlaps for a large collection of strings is a fundamental building block for the analysis of genomic next-generation sequencing data. The approximate suffix-prefix overlap problem is to find all pairs of strings from a given set such that a prefix of one string is similar to a suffix of the other. Välimäki et al. (Information and Computation, 2012) gave a solution to this problem based on suffix filters. In this work, we propose two improvements to the method of Välimäki et al. that reduce the running time of the computation.
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