The statistical significance of nucleotide position-weight matrix matches

Bioinformatics

Volumn 12, Issue 5, 1996, Pages 431-439

  Claverie, Jean Michel ^a   Audic, Stephane ^a  

^a Institute of Structural Biology and Microbiology   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

COMPUTER PROGRAM; CONFERENCE PAPER; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION;

BASE SEQUENCE; FALSE POSITIVE REACTIONS; MATHEMATICAL COMPUTING; PATTERN RECOGNITION, AUTOMATED; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; SOFTWARE; TATA BOX; TRANSCRIPTION, GENETIC;

EID: 0030449157     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.5.431     Document Type: Article

References (24)

1. Altschul.S.F., Gish, W., Miller, W., Myers, E.W. and Lipman.D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Berg, O.G. and von Hippel.P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
3. Brunak, S., Engelbrecht, J. and Knudsen, S. (1991) Prediction of human mRNA donor and acceptor sites from the DAN sequence. J. Mol. Biol., 220, 49-65.
4. Bucher, P. (1990) Weight matrix description of four eukaryotic RNA polymerase II promoter elements derived from 5023 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
5. Claverie, J.M. (1994) Some statistical properties of position/weight matrix scoring systems. Comput. Chem., 18, 287-293.
6. Claverie, J.M. (1996) Exon detection by similarity searches. Methods Mol. Biol, 68.
7. Claverie.J.M. and Sauvaget, I. (1985) Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput. Applic. Bioscl, 1, 95-104.
8. Fickett.J.W. (1996a) The gene identification problem: an overview for developers. Comput. Chem., 20, 103-118.
9. Fickett, J.W. (1996b) Quantitative discrimination of MEF2 sites. Mol. Cell. Biol., 16, 437-441.
10. Gojobori.T., Li, W.-H. and Graur, D. (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol., 18, 360-369.
11. Gribskov, M., Liithy.R. and Eisenberg.D. (1990) Profile analysis. Methods Enzymoi., 183, 146-159.
12. Gumbel.E.J. (1958) Statistics of Extremes. Columbia University Press, New York.
13. Karlin.S. and Altschul.S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. NatlAcad. Sci. USA, 87, 2264-2268.
14. Kulp.D. and Reese.M. (1995) Standard data set for the prediction of genes from human DNA sequences. Available by ftp from: www-hgc.lbl.gov, in directory: /pub/genesets.
15. 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.
16. Li, W.H., Wu, C.-I. and Luo, C.-C. (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol., 21, 58-71.
17. Odenwald, W.F., Garbern, J., Arnheiter.H., Tournier-Lasserve, E. and Lazzarini.R.A. (1989) The HOX-1.3 homeo box protein is a sequence-specific DNA-binding phosphoprotein. Genes Dev., 3, 158-172.
18. Prestridge.D.S. (1995) Predicting Pol II promoter sequences using transcription factor binding sites. J. Mol. Biol., 249, 923-932.
19. Quandt.K., Frech, K., Karas, H., Wingender, E. and Werner.T. (1995) Matlnd and Matlnspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
20. Senapathy.P., Shapiro.M.B. and Harris.N.L. (1990) Splice junctions, branch point sites, and exons: sequence statistics identification, and applications to genome project. Methods Enzymoi., 183, 252-278.
21. Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
22. Staden.R. (1989) Methods for calculating the probabilities of finding patterns in sequences. Comput. Applic. Biosci., 5, 89—96.
23. Stormo, G.D. (1990) Consensus patterns in DNA. Methods Enzymoi, 183, 211-221.
24. Wingender, E., Dietze.P. and Karas.H (1996) 'TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 283-241.