Investigating extended regulatory regions of genomic DNA sequences

Bioinformatics

Volumn 15, Issue 7-8, 1999, Pages 644-653

  Babenko, V N ^a   Kosarev, P S ^a   Vishnevsky, O V ^a   Levitsky, V G ^a   Basin, V V ^a   Frolov, A S ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SYSTEM; CONFERENCE PAPER; CPG ISLAND; DNA SEQUENCE; GENOME; INTERNET; NUCLEOTIDE SEQUENCE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROMOTER REGION; TATA BOX; VERTEBRATE;

EUKARYOTA; VERTEBRATA;

EID: 0032822838     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.7.644     Document Type: Conference Paper

References (52)

1. Allison, L., Edgoose, T. and Dix, T.I. (1998) Compression of Strings with Approximate Repeats. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
2. Allison, L.and Yee, C.N. (1990) Minimum message length encoding and the comparison of macromolecules. Bull. Math. Biol., 52, 431-453.
3. Arratia, R. and Waterman, M.S. (1989) The Erdos-Renyi strong law for pattern matching with a given proportion of mismatches. Ann. Prob., 17, 1152-1169.
4. Baldi, P., Chauvin, Y., Brunak, S., Gorodkin, J. and Pedersen, A.G. (1998) Computational applications of DNA structural scales. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
5. Bucher, P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
6. Bucher, P. and Trifonov, E.N. (1986) Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res., 14, 10009-100026.
7. Chen, Q.K., Hertz, G.Z. and Stormo, G.D. (1995) MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci., 11, 563-566.
8. Clerc, R.G., Bucher, P., Strub, K. and Birnstiel, M.L. (1983) Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the -50 region. Nucleic Acids Res., 11, 8641-8657.
9. Cornish-Bowden, A. (1985) Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res., 13, 3021-3030.
10. Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
11. Frech, K., Hermann, G. and Werner, T. (1993) Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. Nucleic Acids Res., 21, 1655-1664.
12. Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
13. Gelfand, M.S. (1995) Prediction of function in DNA sequence analysis. J. Comp. Biol., 2, 87-115.
14. Grumbach, S, Tahi, F. (1994) A new challenge for compression algorithms: genetic sequences. Inf. Proc. and Management, 30, 875-886.
15. Gusev, V.D., Kulichkov, V.A. and Chupakhina, O.M. (1993) The Lempel-Ziv complexity and local structure analysis of genomes. BioSystems, 30, 183-200.
16. Hutchinson, G.B. (1996) The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput. Appl. Biosci., 12, 391-398.
17. Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A.E., Kel, O.V., Ignatieva, E.V., Ananko, E.A., Podkolodnaya, O.A., Kolpakov, F.A., Podkolodny, N.L. and Kolchanov, N.A. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res., 26, 362-367.
18. Hertz, G. and Stormo, G. (1996) Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol., 273, 30-42.
19. Jurka, J., Klonowski, P., Dagman, V. and Pelton, P. (1996) CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem., 20, 119-122.
20. Karlin, S., Dembo, A. and Kawabata, T. (1990) Statistical composition of high-scoring segments from molecular sequences. Ann. Stat., 18, 571-581.
21. Karlin, S. and Burge, C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet., 11, 283-290.
22. Karlin, S., Ladunga, I. and Blaisdell, B. (1994) Heterogeneity of genomes: measure and values. Proc. Natl Acad. Sci. USA, 91, 12837-12841.
23. Karlin, S., Mrazek, G. and Campbell, A. (1997) Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol., 179, 3899-3913.
24. Kel, A.E., Kolchanov, N.A., Kel, O.V., Romashchenko, A.G., Anan'ko, E.A., Ignat'eva, E.V., Merkulova, T.I., Podkolodnaya, O.A., Stepanenko, I.L., Kochetov, A.V., Kolpakov, F.A., Podkolodnyi, N.L. and Naumochkin, A.A. (1997) TRRD: a database of transcription regulatory regions in eukaryotic genes. Molek. Biol. (Mosk.), 31, 626-636.
25. Kel, O.V., Romaschenko, A.G., Kel, A.E., Kolchanov, N.A. and Wingender, E. (1995) A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res., 23, 4097-4103.
26. Kelly, J.M., Porter, A.C., Chernajovsky, Y., Gilbert, C.S., Stark, G.R. and Kerr, I.M. (1986) Characterization of a human gene inducible by alpha- and beta-interferons and its expression in mouse cells. EMBO J., 5, 1601-1606.
27. Kolchanov N.A., Ananko, E.A., Podkolodnaya, O.A., Ignatieva, E.V., Stepanenko, I.L., Kel-Margoulis, O.V., Kel, A.E., Merkulova, T.I., Goryachkovskaya, T.N., Busigina, T.N., Kolpakov, F.A., Podkolodny, N.L., Naumochkin, A.N. and Romashchenko, A.G. (1999) Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res., 27, 303-306.
28. Kolchanov N.A., Vishnevsky, O.V., Babenko, V.N. and Kel, A.E. (1995) Oligonucleotide Sets. Computer Tool and Application. In Proceedings Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
29. Kolchanov, N.A. and Lim, H.A. (1994) Computer analysis of Genetic Macromolecules.: Structure, Function and Evolution. World Scientific Pub. Co., Singapore, New Jersey, London, Hong Kong.
30. Kolmogorov, A.N. (1965) Three approaches to the quantitative definition of information. Probl. Inf. Transmission, 1, 1-7.
31. Kolpakov, F.A. and Babenko, V.N. (1997) Computer system MGL: a tool for construction of samples, visualization and analysis of genomic regulatory sequences. Molek. Biol. (Mosk.), 31, 647-655.
32. Kondrahin Y.V, Kel, A.E., Kolchanov, N.A., Romaschenko, A.G. and Milanesi, L. (1995) Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci., 11, 477-488.
33. 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.
34. Lempel, A. and Ziv, J. (1976) On the complexity of finite sequences. IEEE Trans. Inf. Theory IT, 22, 783-795.
35. Levitsky, G.V., Ponomarenko, M.P., Ponomarenko, J.V., Frolov, A.S. and Kolchanov, N.A. (1999) Nucleosomal DNA property database. Bioinformatics, 15, 582-592.
36. Milosavljevic, A. and Jurka, J. (1993) Discovering simple DNA sequences by the algorithmic significance method. Comp. Appl. BioSci., 9, 407-411.
37. Nakasone, K., Kenmochi, N., Toku, S. and Tanaka, T. (1993) The structure of the gene encoding chicken ribosomal protein L30. Biochim. Biophys. Acta, 1174, 75-78.
38. Parvin, J.D., McCormick, R.J., Sharp, P.A. and Fisher, D.E. (1995) Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor. Nature, 373, 724-727.
39. Ponomarenko, J.V., Ponomarenko, M.P., Frolov, A.S., Vorobyev, D.G., Overton, G.C. and Kolchanov, N.A. (1999) Conformational and physico-chemical DNA features specific for transcription factor binding sites. Bioinformatics, 15, 654-668.
40. Prestridge, D.S. and Stormo, G. (1993) SIGNAL SCAN 3.0: new database and program features. Comput. Appl. Biosci., 9, 113-115.
41. Prestridge, D.S. (1995) Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol, 249, 923-932.
42. Quandt, K., Frech, K., Karas, H., Wingender, E. and Werner, T. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
43. Quandt, K., Frech, K. and Werner, T. (1997) Analysis of transcription regulatory regions based on recognition of transcription factor binding sites and relative arrangement. Molek. Biol. (Mosk.), 31, 749-758.
44. Roeder, R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci., 21, 327-335.
45. Sazer, S. and Schinike, R.T. (1986) A re-examination of the 5′ termini of mouse dihydrofolate reductase RNA. J. Biol. Chem., 261, 4685-4690.
46. Snyder, E. and Stormo, G. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol., 248, 1-18.
47. Solovyev, V.V., Kolchanov, N.A. and Zhazkikh, A.A. (1994) Method for revealing imperfect repeats in nucleotide sequences. In Kolchanov, N.A. and Lim, H.A. (eds), Computer Analysis of Genetic Macromolecules: Structure, Function and Evolution. World Scientific, Singapore, New Jersey, London, Hong Kong, pp. 107-112.
48. Valerio, D., Duyvesteyn, M.G.C., Dekker, B.M.M., Weeda, G., Berkvens, Th.M., Van der Voorn, L. and Van der Eb, A.J. (1985) Adenosine deaminase: characterization and expression of a gene with remarkable promoter. EMBO J., 4, 437-443.
49. Wingender, E. (1993) Gene Regulation in Eukaryotes. VHC Verlagsgesellschaft mbH, D-69469 Weinheim, Germany.
50. Wingender, E. (1997) Classification of transcription factors in Eukaryotes. Molek. Biol. (Mosk.), 31, 584-600.
51. Wolfertstetter, F., Frech, K., Hermann, G. and Werner, T. (1996) Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Comput. Appl. Biosci., 12, 71-80.
52. Zhang, M.Q. (1998) Identification of human gene core promoters in silico. Genome Res., 8, 319-326.