Genomewide motif Identification using a dictionary model

Proceedings of the IEEE

Volumn 90, Issue 11, 2002, Pages 1803-1810

  Sabatti, Chiara ^a   Lange, Kenneth ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Expectation maximization algorithm; Genomic sequence; Maximum a posteriori; Text segmentation

Indexed keywords

ALGORITHMS; DATA REDUCTION; DATABASE SYSTEMS; MATHEMATICAL MODELS; PROTEINS; RNA;

EXPECTATION-MAXIMIZATION ALGORITHM; GENOMIC SEQUENCE; MAXIMUM A POSTERIORI; TEXT SEGMENTATION;

DNA;

EID: 1342280632     PISSN: 00189219     EISSN: None     Source Type: Journal    
DOI: 10.1109/JPROC.2002.804689     Document Type: Article

References (12)

1. International human genome sequencing consortium, "Initial sequencing and analysis of the human genome," Nature, vol. 409, pp. 860-921, 2001.
2. J. C. Vender et al., "The sequence of the human genome," Science, vol. 291, pp. 1304-1351, 2001.
3. C. E. Lawrence and A. A. Reilly, "An expectation maximization (em) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences," Proteins, vol. 7, pp. 41-51, 1990.
4. C. E. Lawrence, S. F. Altschul, M. S. Bogouski, J. S. Liu, A. F. Neuwald, and J. C. Woolen, "Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment," Science, vol. 262, pp. 208-214, 1993.
5. K. Robison, A. M. McGuire, and G. M. Church, "A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome," J. Mol. Biol., vol. 284, pp. 241-254, 1998.
6. H. J. Bussemaker, H. Li, and E. D. Siggia, "Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis," Proc. Nat. Acad. Sci., vol. 97, pp. 10096-10 100, 2000.
7. _, "Regulatory element detection using a probabilistic segmentation model," in Proc. Int. Conf. Inlell. Syst. Mol. Biol. 8, 2000, pp. 67-74.
8. L. E. Baum, "An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes," Inequalities, vol. 3, pp. 1-8, 1972.
9. P. A. Devijver, "Baum's forward-backward algorithm revisited," Pattern Recognit. Lett., vol. 3, pp. 369-373, 1985.
10. K. Lange, D. R. Hunter, and I. Yang, "Optimization transfer using surrogate objective functions (with discussion)," J. Comput. Graph. Statistics, vol. 9, pp. 1-59, 2000.
11. K. Lange, Mathematical and Statistical Methods for Genetic Analysis, 2nd ed. New York: Springer-Verlag, 2002.
12. L. McCue, A. W. Thompson, C. S. Carmack, M. P. Ryan, J. S. Liu, V. Derbyshire, and C. E. Lawrence, "Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes," Nucleic Acids Res., vol. 29, pp. 774-782, 2001.