Шеленков А.А., Коротков Е.В.
Поиск регулярных последовательностей в промоторах из геномов различных групп организмов с использованием критерия серий
Математическая биология и биоинформатика. 2008;3(1):1-15.
doi: 10.17537/2008.3.1.
Список литературы
- Claverie JM. Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol .Genet. 1997;6:1735-1744. doi: 10.1093/hmg/6.10.1735
- Bajic VB, Chong A, Seah SH, Brusic V. An intelligent system for vertebrate promoter recognition. IEEE Intell. Syst. Mag. 1997;17:64-70.
- Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nature Genet. 2001;29:412-417. doi: 10.1038/ng780
- Ohler U, Liao GC, Niemann H, Rubin GM. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 2002;3:0087.1-0087.12.
- Pedersen AG, Baldi P, Chauvin Y, Brunak S. The biology of Eukaryotic promoter prediction: a review. Comp. Chem. 1999;23:191-207.
- Dieterich С, Grossmann S, Tanzer A, Ropcke S, Arndt PF, Stadler P, Vingron M. Comparative promoter region analysis powered by CORG. BMC Genomics. 2005;6(1):24. doi: 10.1186/1471-2164-6-24
- Bajic VB, Seah SH. Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res. 2003;13:1923-1929.
- Knudsen S. Promoter2.0: for the recognition of PoIII promoter sequences. Bioinformatics. 1999;15:356-361. doi: 10.1093/bioinformatics/15.5.356
- Solovyev VV, Shahmuradov IA. PromH: promoters identification using orthologous genomic sequences. Nucleic Acids Res. 2003;31:3540-3545. doi: 10.1093/nar/gkg525
- Scherf M, Klingenhoff A, Werner T. Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach. J. Mol. Biol. 2000;297:599-606.
- Xie X, Wu S, Lam K-M, Yan H. PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm. Bioinformatics. 2006;22:2722-2728. doi: 10.1093/bioinformatics/btl482
- Matsuyama Y, Kawamura R. Promoter recognition for E. coli DNA segments by independent component analysis. In: Proc. Comput. Syst. Bioinformatics Conf. 2004:686-691.
- Bajic VB, Tan SL, Suzuki Y, Sugano S. Promoter prediction analysis on the whole human genome. Nat. Biotechnol. 2004;22:1467-1473.
- Korotkov EV, Korotkova MA, Kudryashov NA. Information decomposition method to analyze symbolical sequences. Phys. Let. A. 2000;312:198-210.
- Shelenkov AA, Skryabin KG, Korotkov EV. Search and Classification of Potential Minisatellite Sequences from Bacterial Genomes. DNA Res. 2006;13(3):89-102. doi: 10.1093/dnares/dsl004
- Shelenkov AA, Korotkov AE, Korotkov EV. MMsat - a database of potential micro- and minisatellites. Gene. 2008;409:53-60. doi: 10.1016/j.gene.2007.11.007
- Hoel PG. Introduction to Mathematical Statistics, 3rd ed. New-York: Wiley; 1966.
- Brownlee KA. Statistical Theory and Methodology in Science and Engineering. 1984.
- Sheskin DJ. Handbook of Parametric and Nonparametric Statistical Procedures, 2nd ed. New York: Chapman & Hall/CR; 2000.
- Schmid CD, Perier R, Praz V, Bucher P. EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res. 2006;34:D82-85. doi: 10.1093/nar/gkj146
- Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573-580. doi: 10.1093/nar/27.2.573
- Sharma D, Issac B, Raghava GP, Ramaswamy R. Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 2004;20:1405-1412. doi: 10.1093/bioinformatics/bth103
- Werner T. The state of the art of mammalian promoter recognition. Brief Bioinform. 2003;4 (1):22-30. doi: 10.1093/bib/4.1.22
- Fickett JW, Hatzigeorgiou AG. Eukaryotic promoter recognition. Genome Res. 1997;7(9):861-878.
- Novichkov PS, Gelfand MS, Mironov AA. Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics. 2001;17(11):1011-1018. doi: 10.1093/bioinformatics/17.11.1011
- Hertel KJ. Combinatorial control of exon recognition. J. Biol Chem. 2008;283(3):1211-1215. doi: 10.1074/jbc.R700035200
- Zhang MQ. Computational analyses of eukaryotic promoters. BMC Bioinformatics. 2007;8(6):S3. doi: 10.1186/1471-2105-8-S6-S3
- Ioshikhes I, Trifonov EN, Zhang MQ. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc Natl Acad Sci USA. 1999;96(6):2891-2895. doi: 10.1073/pnas.96.6.2891
- Kutuzova GI, Frank GK, Makeev VIu, Esipova NG, Polozov RV. Fourier analysis of nucleotide sequences. Periodicity in E. coli promoter sequences. Biofizika. 1997;42(2):354-362.
- Tchernaenko V, Radlinska M, Lubkowska L, Halvorson HR, Kashlev M, Lutter LC. DNA bending in transcription initiation. Biochemistry. 2008;47(7):1885-1895. doi: 10.1021/bi7012883
- Mizuno T. Static bend of DNA helix at the activator recognition site of the ompF promoter in Escherichia coli. Gene. 1987;54:57-64. doi: 10.1016/0378-1119(87)90347-7
- Bolshoy A, Nevo E. Ecologic genomics of DNA: upstream bending in prokaryotic promoters. Genome Res. 2000;10:1185-1193. doi: 10.1101/gr.10.8.1185
- Ozoline ON, Deev AA, Trifonov EN. DNA bendability - a novel feature in E. coli promoter recognition. J. Biomol Struct Dyn. 1999;16(4):825-31. doi: 10.1080/07391102.1999.10508295
|
|
|