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Panoptic Motif Search



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  1. Marius Nicolae and Sanguthevar Rajasekaran. "qPMS9: An Efficient Algorithm for Quorum Planted Motif Search". Scientific reports 5 (2015). [link] [qPMS9 source code and test datasets]

  2. Marius Nicolae and Sanguthevar Rajasekaran. "Efficient sequential and parallel algorithms for planted motif search". BMC bioinformatics 15.1 (2014): 34. [link] [PMS8 source code] [PMS8 test datasets]

  3. Hieu Dinh and Sanguthevar Rajasekaran and Jaime Davila. "qPMS7: A Fast Algorithm for Finding (l, d)-Motifs in DNA and Protein Sequences". PLOS One. July 2012. [link] [full text]

  4. Hieu Dinh and Sanguthevar Rajasekaran and Vamsi K Kundeti. "PMS5: an efficient exact algorithm for the (l, d)-motif finding problem". BMC Bioinformatics. October 2011. [link] [full text]

  5. Sanguthevar Rajasekaran and Hieu Dinh. "A Speedup Technique for (l,d)-Motif Finding Algorithms". BMC Research Notes. March 2011. [link] [full text]

  6. S. Rajasekaran. "Computational techniques for motif search". Frontiers in Bioscience. June 1, 2009, pp. 5052-5065. [link]

  7. D. Sharma and S. Rajasekaran. "A simple algorithm for (l,d)-motif search". Proc. International IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2009, March 30-April 2, Nashville, TN. [link]

  8. J. Davila, S. Balla, and S. Rajasekaran. "Fast and practical algorithms for planted (l,d) motif search". IEEE/ACM Transactions on Computational Biology and Bioinformatics. October 2007, pp. 544-552. [link] [full text]

  9. S. Rajasekaran, S. Balla, and C.-H. Huang. "Exact algorithms for planted motif challenge problems". Journal of Computational Biology. 12(8), 2005, pp. 1117-1128. [link] [full text]

Download software

 
  • qPMS9 can handle input instances up to (25,10) on a desktop computer or larger instances on multi-core computers. Download qPMS9 here. If your use qPMS9 in your research, please cite this paper:

    M. Nicolae, and S. Rajasekaran. "qPMS9: An Efficient Algorithm for Quorum Planted Motif Search". Scientific reports 5 (2015). [link]

  • PMS8 is an earlier version of the (recommended) qPMS9. Download PMS8 source code here. Download PMS8 test datasets here. If your use PMS8 in your research, please cite this paper:

    M. Nicolae, and S. Rajasekaran. "Efficient sequential and parallel algorithms for planted motif search". BMC bioinformatics 15.1 (2014): 34. [link]

  • PMS5 can handle input instances up to (23,9) on a desktop computer. Download PMS5 executable program on Windows here. If your use PMS5 in your research, please cite this paper:

    H. Dinh, S. Rajasekaran, and V. Kundeti. "PMS5: an efficient exact algorithm for the (l, d)-motif finding problem". BMC Bioinformatics. October 2011. [link] [full text]

  • PMSPrune can handle input instances up to (19,7) on a desktop computer. Download PMSPrune source code in C here. Download PMSPrune executable program on Windows here. If your use PMSPrune in your research, please cite this paper:

    J. Davila, S. Balla, and S. Rajasekaran. "Fast and practical algorithms for planted (l,d) motif search". IEEE/ACM Transactions on Computational Biology and Bioinformatics. October 2007, pp. 544-552. [link] [full text]

  • PMS1 can handle input instances up to (15,5) on a desktop computer. Download PMS1 source code in C here. Download PMS1 executable program on Windows here. If your use PMS1 in your research, please cite this paper:

    S. Rajasekaran, S. Balla, and C.-H. Huang. "Exact algorithms for planted motif challenge problems". Journal of Computational Biology. 12(8), 2005, pp. 1117-1128. [link] [full text]

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