PMS Panoptic Motif Search

• Online motif search tools
  
  • Finding de-novo DNA motif sequences

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  • Finding de-novo Protein motif sequences

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• Submission history

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• Help

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• Feedback

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• Download

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• Sponsors and fundings

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• About us

Useful Links

External Links

• University of Connecticut

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• Computer Science and Engineering Department

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• BECAT: Booth Engineering Center for Advanced Technology

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• Online Motif Discovery Tools

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• MnM: Advance Mimimotif Miner

1. 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]

2. 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]

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

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

5. 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]

6. 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]

7. 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]

• 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]