An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, ISMB 2000

Volumn , Issue , 2000, Pages 37-45

  Blanchette, Mathieu ^a   Schwikowski, Benno ^a   Tompa, Martin ^a  

^a University of Washington   (United States)

Author keywords

algorithm; motif; orthologous; phylogeny; promoter; sequence analysis

Indexed keywords

ARTIFICIAL INTELLIGENCE; BINDING SITES;

EXACT ALGORITHMS; MOTIF; MULTIPLE SPECIES; ORTHOLOGOUS; ORTHOLOGOUS SEQUENCES; PHYLOGENY; PROMOTER; SEQUENCE ANALYSIS; SEQUENCE MOTIFS; SPLICE SITE;

GENES;

ALGORITHM; ANIMAL; ARTICLE; GENOME; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

ALGORITHMS; ANIMALS; BASE SEQUENCE; GENOME; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS; SPECIES SPECIFICITY;

EID: 0034565406     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (31)

1. Akutsu, T. 1998. Hardness results on gapless local multiple sequence alignment. Technical Report 98-MPS-24-2, Information Processing Society of Japan.
2. Arguello-Astorga, G., and Herrera-Estrella, L. 1998. Evolution of light-regulated plant promoters. Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:525-555.
3. Bailey, T. L., and Elkan, C. 1995. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21 (l-2) :51-80.
4. Brāzma, A.; Jonassen, I.; Vilo, J.; and Ukkonen, E. 1998. Predicting gene regulatory elements in silico on a genomic scale. Genome Research 15:1202-1215.
5. Caprara, A. 1997. Sorting by reversals is difficult. In RECOMB97: Proceedings of the First Annual International Conference on Computational Molecular Biology, 75-83.
6. Chu, S.; DeRisi, J.; Eisen, M.; Mulholland, J.; Botstein, D.; Brown, P. O.; and Herskowitz, I. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705.
7. Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22:521-565.
8. Fitch, W. M., and Margoliash, E. 1967. Construction of phylogenetic trees. Science 155:279-284.
9. Fitch, W. M. 1971. Toward denning the course of evolution: Minimum change for a specified tree topology. Systematic Zoology 20:406-416.
10. Flybase. http://flybase.bio.indiana.edu
11. Fraenkel, Y. M.; Mandel, Y.; Friedberg, D.; and Margalit, H. 1995. Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Computer Applications in the Biosciences 11 (4) :379-387.
12. Galas, D. J.; Eggert, M.; and Waterman, M. S. 1985. Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli. Journal of Molecular Biology 186 (1) :117-128.
13. Genbank. http://www.ncbi.nlm.nih.gov/Genbank
14. Hertz, G. Z., and Stormo, G. D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 (7/8) :563-577.
15. Higgins, D. G.; Thompson, J. D.; and Gibson, T. J. 1996. Using CLUSTAL for multiple sequence alignments. In Doolittle, R. F., ed., Computer Methods for Macromolecular Sequence Analysis, volume 266 of Methods in Enzymology. New York: Academic Press. 383-401.
16. Kerlavage, A. R. 1999. Computational genomics: Biological discovery in complete genomes. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, xii. Heidelberg, Germany: AAAI Press.
17. Klegg, M. T. 1993. Chloroplast gene sequences and the study of plant evolution. Proceedings of the National Academy of Science USA 90 (2) :363-367.
18. Lawrence, C. E., and Reilly, A. A. 1990. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function, and Genetics 7:41-51.
19. Lawrence, C. E.; Altschul, S. F.; Boguski, M. S.; Liu, J. S.; Neuwald, A. F.; and Wootton, J. C. 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262:208-214.
20. Magnuson, M., and Shelton, K. 1989. An alternate promoter in the glucokinase gene is active in the pancreatic beta cell. Journal of Biological Chemistry 264 (27) :15936-15942.
21. Magnuson, M., and Thomas, J. 1993. Evolutionary conservation of elements in the upstream glucokinase promoter. Biochem. Soc. Trans. 21 (1) :160-163.
22. Manen, J. F.; Savolainen, V.; and Simon, P. 1994. The atpB and rbcL promoters in plastid DNAs of a wide dicot range. Journal of Molecular Evolution 38 (6) :577-582.
23. Moses, K.; Heberlein, U.; and Ashburner, M. 1990. The adh gene promoters of Drosophila melanogaster and Drosophila orena are functionally conserved and share features of sequence structure and nuclease-protected sites. Molecular and Cellular Biology 10 (2) :539-548.
24. Roth, F. P.; Hughes, J. D.; Estep, P. W.; and Church, G. M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16:939-945.
25. Sankoff, D., and Rousseau, P. 1975. Locating the vertices of a Steiner tree in arbitrary metric space. Mathematical Programming 9:240-246.
26. Shine, J., and Dalgarno, L. 1974. The 3'-terminal sequence of E. coli 16S ribosomal RJNTA: Complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Science USA 71:1342-1346.
27. Sinha, S., and Tompa, M. 2000. A statistical method for finding transcription factor binding sites. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. San Diego, CA: AAAI Press.
28. Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; Iyer, V. R.; Anders, K.; Eisen, M. B.; Brown, P. O.; Botstein, D.; and Futcher, B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9:3273-3297.
29. Staden, R. 1989. Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in the Biosciences 5 (4) :293-298.
30. Tavazoie, S.; Hughes, J. D.; Campbell, M. J.; Cho, R. J.; and Church, G. M. 1999. Systematic determination of genetic network architecture. Nature Genetics 22:281-285.
31. van Helden, J.; André, B.; and Collado-Vides, J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 281 (5) :827-842.