A novel method for prokaryotic promoter prediction based on DNA stability

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Kanhere, Aditi ^a   Bansal, Manju ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA STABILITY; GENE PREDICTION; GENOME ANNOTATION; GENOMIC REGIONS; PROKARYOTIC PROMOTERS; PROMOTER PREDICTION; PROMOTER REGION; SEQUENCE MOTIFS;

DNA; ESCHERICHIA COLI; GENES; STABILITY;

FORECASTING;

DNA; RNA;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENOME; COMPUTER PROGRAM; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; DNA DETERMINATION; DNA SEQUENCE; ESCHERICHIA COLI; EUKARYOTE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC CODE; GENOMICS; MATHEMATICAL COMPUTING; NONHUMAN; PREDICTION; PROKARYOTE; PROMOTER REGION; PROTEIN MOTIF; BACTERIAL GENE; BIOLOGY; CHEMISTRY; GENETIC TRANSCRIPTION; GENETICS; PROCEDURES; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; THERMODYNAMICS;

ESCHERICHIA COLI; PROKARYOTA;

AMINO ACID MOTIFS; BACILLUS SUBTILIS; COMPUTATIONAL BIOLOGY; CORYNEBACTERIUM GLUTAMICUM; DNA; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; MODELS, STATISTICAL; PROMOTER REGIONS, GENETIC; RNA; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 13244287791     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-6-1     Document Type: Article

References (39)

1. Fickett JW: The gene identification problem: An overview for developers. Comput Chem 1996, 20:103-118.
2. Claverie JM: Computational methods for the identification of genes in vertebrate genomic sequences. Hum Mol Genet 1997, 6:1735-1744.
3. Stormo GD: Gene-finding approaches for eukaryotes. Genome Res 2000, 10:394-397.
4. Mathé C, Sagot MF, Schiex T, Rouzé P: Current methods of gene prediction, their strength and weaknesses. Nucleic Acids Res 2002, 30:4103-4117.
5. Zhang MQ: Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 2002, 3:698-709.
6. Fickett JW, Hatzigeorgiou AG: Eukaryotic promoter recognition. Genome Res 1997, 7:861-78.
7. Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, van de Peer Y: Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol 2003, 132:1162-1176.
8. Werner T: The state of the art of mammalian promoter recognition. Brief Bioinform 2003, 4:22-30.
9. Pedersen AG, Baldi P, Chauvin Y, Brunak S: The biology of eukaryotic promoter prediction - a review. Comput Chem 1999, 23:191-207.
10. Kanhere A, Bansal M: Identifcation of additional 'punctuation marks' in genomic DNA [abstract]. In proceedings of 10th congress of FAOBMB: Bangalore :139. 7-11 December 2003
11. Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL: Helix stability in prokaryotic promoter regions. Biochemistry 1988, 27:5179-5188.
12. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW: A DNA structural atlas for Escherichia coli. J Mol Biol 2000, 299:907-930.
13. Choi CH, Kalosakas G, Rasmussen KO, Hiromura M, Bishop AR, Usheva A: DNA dynamically directs its own transcription initiation. Nucleic Acids Res 2004, 32:1584-1590.
14. Levitskii VG, Katokhin AV: Computer analysis and recognition of Drosophila melanogaster gene promoters. Mol Biol (Mosk) 2001, 35:970-978.
15. Lisser S, Margalit H: Determination of common structural features in Escherichia coli promoters by computer analysis. Eur J Biochem 1994, 223:823-830.
16. Nakata K, Kanehisa M, Maizel JV Jr: Discriminant analysis of promoter regions in Escherichia coli sequences. Comput Appl Biosci 1988, 4:367-71.
17. Vollenweider HJ, Fiandt M, Szybalski W: A relationship between DNA helix stability and recognition sites for RNA polymerase. Science 1979, 205:508-511.
18. Breslauer KJ, Frank R, Blocker H, Marky LA: Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750.
19. Reese MG: Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 2001, 26:51-56.
20. NNPP [http://www.fruitfly.org/seq_tools/promoter.html]
21. Staden R: Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res 1984, 12:505-519.
22. Mulligan ME, Hawley DK, Entriken R, McClure WR: Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res 1984, 12:789-800.
23. Alexandrov NN, Mironov AA: Application of a new method of pattern recognition in DNA sequence analysis: a study of E. coli promoters. Nucleic Acids Res 1990, 18:1847-1852.
24. Huerta AM, Collado-Vides J: Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol 2003, 333: 61-278.
25. Burden S, Lin YX, Zhang R: Improving promoter prediction for the NNPP2.2 algorithm: a case study using E. coli DNA sequences. Bioinformatics 2004 in press.
26. Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M: Predicting bacterial transcription units using sequence and expression data. Bioinformatics 2003, 19(Suppl 1):i34-43.
27. Ohler U, Niemann H, Liao G, Rubin GM: Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 2001, 17(Suppl 1):S199-206.
28. Hutchinson GB: The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Comput Appl Biosci 1996, 12:391-398.
29. Escherichia coli RNA genes at NCBI [http://www.ncbi.nlm.nih.gov/genomes/rnatab.cgi?gi=115&db=Genome]
30. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S: Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001, 11:941-950.
31. Hershberg R, Bejerano G, Santos-Zavaleta A, Margalit H: PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res 2001, 29:277.
32. Makita Y, Nakao M, Ogasawara N, Nakai K: DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res 2004, 32(Database):D75-77.
33. Pàtek M, Nesvera J, Guyonvarch A, Reyes O, Leblon G: Promoters of Corynebacterium glutamicum. J Biotechnol 2003, 104:311-323.
34. SantaLucia J Jr: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998, 95:1460-1465.
35. Allawi HT, SantaLucia J Jr: Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 1997, 36: 0581-10594.
36. Young IT: Proof without prejudice: use of the Kolmogorov-Smirnov test for the analysis of histograms from flow systems and other sources. J Histochem Cytochem 1977, 25:935-941.
37. Hertz GZ, Stormo GD: Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol 1996, 273:30-42.
38. Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
39. van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res 2003, 31:3593-3596.