An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets
暂无分享,去创建一个
[1] Michael B. Yaffe,et al. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs , 2003, Nucleic Acids Res..
[2] Charles Elkan,et al. Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.
[3] Yun Xu,et al. An improved voting algorithm for planted (l, d) motif search , 2013, Inf. Sci..
[4] Marie-France Sagot,et al. RISOTTO: Fast Extraction of Motifs with Mismatches , 2006, LATIN.
[5] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[6] Qiang Yu,et al. A Heuristic Cluster-Based EM Algorithm for the Planted (L, d) Problem , 2013, J. Bioinform. Comput. Biol..
[7] P. D’haeseleer. What are DNA sequence motifs? , 2006, Nature Biotechnology.
[8] Eric S. Ho,et al. iTriplet, a rule-based nucleic acid sequence motif finder , 2009, Algorithms for Molecular Biology.
[9] Eleazar Eskin,et al. Finding composite regulatory patterns in DNA sequences , 2002, ISMB.
[10] Sanguthevar Rajasekaran,et al. Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences , 2011, Nucleic Acids Res..
[11] Richard J. Edwards,et al. ELM—the database of eukaryotic linear motifs , 2011, Nucleic Acids Res..
[12] Richard J. Edwards,et al. SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins , 2007, PloS one.
[13] Jeffrey Scott Vitter,et al. StemFinder: An efficient algorithm for searching motif stems over large alphabets , 2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine.
[14] Qiang Yu,et al. PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search , 2012, PloS one.
[15] Pavel A. Pevzner,et al. Combinatorial Approaches to Finding Subtle Signals in DNA Sequences , 2000, ISMB.
[16] Francis Y. L. Chin,et al. Voting algorithms for discovering long motifs , 2005, APBC.
[17] Vladimir Pavlovic,et al. Efficient motif finding algorithms for large-alphabet inputs , 2010, BMC Bioinformatics.
[18] D UllmanJeffrey,et al. Introduction to automata theory, languages, and computation, 2nd edition , 2001 .
[19] Sanguthevar Rajasekaran,et al. Efficient algorithms for biological stems search , 2013, BMC Bioinformatics.
[20] Richard J. Edwards,et al. SLiMSearch 2.0: biological context for short linear motifs in proteins , 2011, Nucleic Acids Res..
[21] T. D. Schneider,et al. Consensus sequence Zen. , 2002, Applied bioinformatics.
[22] Sanguthevar Rajasekaran,et al. PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem , 2011, BMC Bioinformatics.
[23] Graziano Pesole,et al. An algorithm for finding signals of unknown length in DNA sequences , 2001, ISMB.
[24] Jun S. Liu,et al. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.
[25] Todd Wareham,et al. On the complexity of finding common approximate substrings , 2003, Theor. Comput. Sci..
[26] Zhi-Zhong Chen,et al. Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)-Motif Model , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[27] Sanguthevar Rajasekaran,et al. Minimotif miner 2nd release: a database and web system for motif search , 2008, Nucleic Acids Res..
[28] Sanguthevar Rajasekaran,et al. qPMS7: A Fast Algorithm for Finding (ℓ, d)-Motifs in DNA and Protein Sequences , 2012, PloS one.
[29] Jeffrey D. Ullman,et al. Introduction to Automata Theory, Languages and Computation , 1979 .
[30] Sanguthevar Rajasekaran,et al. Achieving High Accuracy Prediction of Minimotifs , 2012, PloS one.
[31] Jaime I. Dávila,et al. Fast and Practical Algorithms for Planted (l, d) Motif Search , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[32] Richard J. Edwards,et al. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs , 2010, Nucleic Acids Res..
[33] Vladimir Pavlovic,et al. Fast Motif Selection for Biological Sequences , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine.