Abstract
A Structured Motif refers to a sequence of simple motifs with distance constraints. We present SimpLiSMS, a simple, lightweight and fast algorithm for searching structured motifs. SimpLiSMS does not use any sophisticated data structure, which makes it simple and lightweight. Our experiments show excellent performance of SimpLiSMS. Furthermore, we introduce a parallel version of SimpLiSMS which runs even faster.
Part of this research has been supported by an INSPIRE Strategic Partnership Award, administered by the British Council, Bangladesh for the project titled “Advances in Algorithms for Next Generation Biological Sequences”.
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Alatabbi, A., Azmin, S., Habib, M.K., Iliopoulos, C.S., Rahman, M.S. (2015). SimpLiSMS: A Simple, Lightweight and Fast Approach for Structured Motifs Searching. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9044. Springer, Cham. https://doi.org/10.1007/978-3-319-16480-9_22
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DOI: https://doi.org/10.1007/978-3-319-16480-9_22
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