Asian Journal of Information Technology

Year: 2016
Volume: 15
Issue: 23
Page No. 4835 - 4843

Improved Exact Parallel Algorithm for Planted (l, d) Motif Search

Authors : Satarupa Mohanty and Biswajit Sahoo

References

Bandyopadhyay, S., S. Sahni and S. Rajasekaran, 2014. PMS6: A fast algorithm for motif discovery. Intl. J. Bioinf. Res. Appl., 10: 369-383.
Direct Link  |  

Buhler, J. and M. Tompa, 2002. Finding motifs using random projections. J. Comput. Biol., 9: 225-242.
CrossRef  |  Direct Link  |  

Chin, F.Y. and H.C. Leung, 2005. Voting Algorithms for Discovering Long Motifs. In: Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, Yi-Ping, P.C. and W. Limsoon (Eds.). Imperial College Press, London, UK., pp: 261-271.

Davila, J., S. Balla and S. Rajasekaran, 2006. Space and time efficient algorithms for planted motif search. Proceedings of the International Conference on Computational Science, May 28-31, 2006, Springer, Berlin, Germany, pp: 822-829.

Davila, J., S. Balla and S. Rajasekaran, 2007. Fast and practical algorithms for planted (l, d) motif search. IEEE/ACM. Trans. Comput. Biol. Bioinf., 4: 544-552.
CrossRef  |  Direct Link  |  

Davila, J., S. Balla and S. Rajasekaran, 2007. Pampa: An improved branch and bound algorithm for planted (l, d) motif search. Master Thesis, University of Connecticut, Mansfield, Connecticut. https://pdfs.semanticscholar.org/d54a/d28de70daaf73e59f8334f182d7524187d7c.pdf.

Dinh, H., S. Rajasekaran and J. Davila, 2012. qPMS7: A fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences. PloS One, Vol. 7,

Dinh, H., S. Rajasekaran and V.K. Kundeti, 2011. PMS5: An efficient exact algorithm for the (ℓ, d)-motif finding problem. BMC. Bioinf., 12: 410-410.
CrossRef  |  Direct Link  |  

Eskin, E. and P.A. Pevzner, 2002. Finding composite regulatory patterns in DNA sequences. Bioinf., 18: S354-S363.
Direct Link  |  

Evans, P.A. and A.D. Smith, 2003. Toward optimal motif enumeration. Proceedings of the Workshop on Algorithms and Data Structures, July 30-August 1, 2003, Springer, Berlin, Germany, pp: 47-58.

Evans, P.A., A.D. Smith and H.T. Wareham, 2003. On the complexity of finding common approximate substrings. Theor. Comput. Sci., 306: 407-430.
Direct Link  |  

Herts, G.Z. and G.D. Stormo, 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15: 563-577.
Direct Link  |  

Huang, C.W., W.S. Lee and S.Y. Hsieh, 2011. An improved heuristic algorithm for finding motif signals in DNA sequences. IEEE/ACM. Trans. Comput. Biol. Bioinf., 8: 959-975.
CrossRef  |  Direct Link  |  

Keich, U. and P. Pevzner, 2002. Finding motifs in the twilight zone. Bioinf., 18: 1374-1381.

Lawrence, C.E., S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Newald and J.C. Wootton, 1993. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignments. Science, 262: 208-214.
Direct Link  |  

Nicolae, M. and S. Rajasekaran, 2014. Efficient sequential and parallel algorithms for planted motif search. BMC. Bioinf., 15: 1-34.
CrossRef  |  Direct Link  |  

Nicolae, M. and S. Rajasekaran, 2015. qPMS9: An efficient algorithm for quorum planted motif search. MSc Thesis, University of Connecticut, Mansfield, Connecticut.

Pavesi, G., G. Mauri and G. Pesole, 2001. An algorithm for finding signals of unknown length in DNA sequences. Bioinf., 17: S207-S214.
PubMed  |  Direct Link  |  

Pevzner, P. and S.J. Sze, 2000. Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, San Diego, CA., USA., pp: 268-278.

Pisanti, N., A.M. Carvalho, L. Marsan and M.F. Sagot, 2006. RISOTTO: Fast extraction of motifs with mismatches. Proceedings of the Latin American Symposium on Theoretical Informatics, March 20-24, 2006, Springer, Berlin, Germany, pp: 757-768.

Price, A., S. Ramabhadran and P.A. Pevzner, 2003. Finding subtle motifs by branching from sample strings. Bioinf., 19: ii149-ii155.
Direct Link  |  

Rajasekaran, S. and H. Dinh, 2011. A speedup technique for (l, d)-motif finding algorithms. BMC. Res. Notes, 4: 54-54.
CrossRef  |  Direct Link  |  

Rajasekaran, S., S. Balla and C.H. Huang, 2005. Exact algorithms for planted motif problems. J. Comput. Biol., 12: 1117-1128.
CrossRef  |  Direct Link  |  

Rocke, E. and M. Tompa, 1998. An algorithm for finding novel gapped motif in DNA sequences. Proceedings of the 2nd Annual International Conference on Computational Molecular Biology, March 22-25, 1998, New York, USA., pp: 228-233.

Sagot, M.F., 1998. Spelling approximate repeated or common motifs using a suffix tree. Proceedings of the Latin American Symposium on Theoretical Informatics, April 20-24, 1998, Springer, Berlin, Germany, pp: 374-390.

Sun, H.Q., M.Y.H. Low, W.J. Hsu and J.C. Rajapakse, 2010. ListMotif: A time and memory efficient algorithm for weak motif discovery. Proceedings of the 2010 International Conference on Intelligent Systems and Knowledge Engineering (ISKE), November 15-16, 2010, IEEE, New York, USA., ISBN:978-1-4244-6793-8, pp: 254-260.

Sun, H.Q., M.Y.H. Low, W.J. Hsu and J.C. Rajapakse, 2010. RecMotif: A novel fast algorithm for weak motif discovery. BMC. Bioinf., 11L: S8-S8.
Direct Link  |  

Sun, H.Q., M.Y.H. Low, W.J. Hsu, C.W. Tan and J.C. Rajapakse, 2011. Tree-structured algorithm for long weak motif discovery. Bioinf., 27: 2641-2647.
Direct Link  |  

Sze, S.H. and X. Zhao, 2007. Improved pattern-driven algorithms for motif finding in DNA sequences. Proceedings of the Conference on Systems Biology and Regulatory Genomics, December 2-4, 2005, Springer, Berlin, Germany, pp: 198-211.

Sze, S.H., S. Lu and J. Chen, 2004. Integrating sample-driven and pattern-driven approaches in motif finding. Proceedings of the International Workshop on Algorithms in Bioinformatics, September 17-21, 2004, Springer, Berlin, Germany, pp: 438-449.

Yang, X. and J.C. Rajapakse, 2004. Graphical approach to weak motif recognition. Genome Inf., 15: 52-62.
PubMed  |  Direct Link  |  

Yu, Q., H. Huo, Y. Zhang and H. Guo, 2012. PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search. PLoS One, Vol. 7,

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