Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm

Bioinformatics

Volumn 12, Issue 1, 1996, Pages 71-80

  Wolfertstetter, Franz ^a   Freeh, Kornelie ^a   Herrmann, Gunter ^a   Werner, Thomas ^a  

^a GSF Forschungszentrum fiir Umwelt und Gesundheil GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BINDING SITE; DNA SEQUENCE; LONG TERMINAL REPEAT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; TATA BOX;

ALGORITHMS; BASE SEQUENCE; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; DATABASES, FACTUAL; DNA; EVALUATION STUDIES; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0029867505     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.1.71     Document Type: Article

References (19)

1. Alcxandrov.N. and Mironov.A. (1990) Application of a new method of pattern recognition in DNA sequence analysis: a study of E.coli promoters. Nucleic Acids Res., 18, 1847-1852.
2. Angel.P., Hattori.K., Smeal.T. and Karin.M. (1988) The jun proto-oncogene is positively autorcgulated by its product. Jun/AP-1. Cell, 55. 875-885.
3. Bucher.P. and Bryan, B. (1984) Signal search: a new method to localize and characterize functionally important DNA. Nucleic Acids Res., 12. 287-305.
4. Cardon, L.R. and Stormo, G.D. (1992) Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J. Mol. Biol., 223, 159-170.
5. Etzerodt, M., Mikkelsen, T., Pedersen.F.S., Kjeldgaard, N.O. and Jorgen-sen.P. (1984) The nucleotide sequence of the Akv murinc leukemia virus genome. Virology, 134, 196-207.
6. Freeh, K., Herrmann, G. and Werner.T. (1993) Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. Nucleic Acids Res., 21, 1655-1664.
7. Galas, D.J., Eggert, M. and Waterman, M.S. (1985) Rigorous pattern-recognition methods for DNA sequences. J. Mol. Biol., 186. 117-128.
8. Gartmann, C.J. and Grob, U. (1991) SQUIRREL: Sequence Query. Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX. Nucleic-Acids Res., 19, 6033-6040.
9. GoodrichJ.A., Schwartz, M.L. and McClure.W.R. (1990) Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHFJ. Nucleic Acids Res., 18. 4993-5000.
10. Herr, W. (1984) Nucleotide sequence of AKV murine leukemia virus. J. Virol., 49, 471-478.
11. Hertz.G.Z., Hartzell III, G.W., Stormo.G.D. (1990) Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Applic. Biosci., 6, 81-92.
12. 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 Genetics, 7, 41-51.
13. Liuni, S., Prunella.N., Pesole, G., Dorazio, T., Stella, E. and Distante.A. (1993) SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences. Comput. Applic. Biosci., 9, 701-707.
14. Majors, J. (1990a) The structure and function of retroviral long terminal repeats. Curr. Topics in Microbiol. Immunol., 157, 50-79.
15. Majors, J. (1990b) Retroviruses, strategies of replication: The structure and function of retroviral long terminal repeats, In Swanstrom R. and Vogt P.K. (eds) Springer-Verlag.
16. McLauchlan, J., Gaffney, D., Whitton.L.J. and ClementsJ.B. (1985) The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini. Nucleic Acids Res., 13, 1347-1368.
17. Mengeritsky, G. and Smith, T.F. (1987) Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput. Applic. Biosci., 3, 223-227.
18. Pesole, G., Prunella, N., Liuni, S., Attimonelli, M. and Saccone.C. (1992) WORDUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences. Nucleic Acids Res., 20, 2871-2875.
19. Stormo, G.D. and Hartzell, G.W. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA. 86. 1183-1187.