Abstract
We study the problem of structured motif search in DNA sequences. This is a fundamental task in bioinformatics which contributes to better understanding of genome characteristics and properties. We propose an efficient algorithm for Exact Match, Overlapping Structured motif search (EMOS), which uses a suffix tree index we proposed earlier and runs on a typical desktop computer. We have conducted numerous experiments to evaluate EMOS and compared its performance with the best known solution, SMOTIF1 [1]. While in some cases the search time of EMOS is comparable to SMOTIF1, it is on average 5 to 6 times faster.
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Halachev, M., Shiri, N. (2008). Fast Structured Motif Search in DNA Sequences. In: Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C. (eds) Bioinformatics Research and Development. BIRD 2008. Communications in Computer and Information Science, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70600-7_5
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DOI: https://doi.org/10.1007/978-3-540-70600-7_5
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