Abstract
A challenging variant of the motif finding problem (MFP) is called planted (l,d)-motif finding. It is where the pattern has expected number of mismatches on each of its occurrence in the sequence. Difficulty arises when the planted pattern is longer and the expected number of mismatches is high. An algorithm (FMURP) which uses a random projection technique followed by local search algorithms is shown to work better with longer motifs with higher accuracy. A parallel algorithm for FMURP already exist in the literature. However, the parallel algorithm uses an excessive amount of memory. In this paper, we propose some improvements on the existing parallel algorithm. We also prove that the modified parallelization is equivalent to the sequential version of FMURP.
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Clemente, J.B., Adorna, H.N. (2013). Some Improvements of Parallel Random Projection for Finding Planted (l,d)-Motifs. In: Nishizaki, Sy., Numao, M., Caro, J., Suarez, M.T. (eds) Theory and Practice of Computation. Proceedings in Information and Communications Technology, vol 7. Springer, Tokyo. https://doi.org/10.1007/978-4-431-54436-4_5
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DOI: https://doi.org/10.1007/978-4-431-54436-4_5
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-54435-7
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