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Volumn 25, Issue 16, 2009, Pages 2006-2012

A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; CPG ISLAND; DNA STRUCTURE; GENE SEQUENCE; HUMAN; K NEAREST NEIGHBOR; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SPECIES DIFFERENCE;

EID: 68549098194     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp359     Document Type: Article
Times cited : (24)

References (34)
  • 1
    • 39049168212 scopus 로고    scopus 로고
    • Generic eukaryotic core promoter prediction using structural features of DNA
    • Abeel,T. et al. (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res., 18, 310-323.
    • (2008) Genome Res , vol.18 , pp. 310-323
    • Abeel, T.1
  • 2
    • 0042525750 scopus 로고    scopus 로고
    • Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units
    • Bajic,V.B. and Seah,S.H. (2003) Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res., 13, 1923-1929.
    • (2003) Genome Res , vol.13 , pp. 1923-1929
    • Bajic, V.B.1    Seah, S.H.2
  • 3
    • 8344288229 scopus 로고    scopus 로고
    • Promoter prediction analysis on the whole human genome
    • Bajic,V.B. et al. (2004) Promoter prediction analysis on the whole human genome. Nat. Biotechnol., 22, 1467-1473.
    • (2004) Nat. Biotechnol , vol.22 , pp. 1467-1473
    • Bajic, V.B.1
  • 4
    • 0031614136 scopus 로고    scopus 로고
    • Computational applications of DNA structural scales
    • Baldi,P. et al. (1998) Computational applications of DNA structural scales. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6 35-42.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.6 , pp. 35-42
    • Baldi, P.1
  • 5
    • 30544442885 scopus 로고    scopus 로고
    • Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence
    • Berezhnoy,A.Y. and Shckorbatov,Y.G. (2005) Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence. J. Zhejiang Univ. SCI., 6B11, 1063-1068.
    • (2005) J. Zhejiang Univ. SCI , vol.6 B11 , pp. 1063-1068
    • Berezhnoy, A.Y.1    Shckorbatov, Y.G.2
  • 7
    • 0001550068 scopus 로고
    • Predicting DNA duplex stability from the base sequence
    • Breslauer,K.J. et al. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
    • (1986) Proc. Natl Acad. Sci. USA , vol.83 , pp. 3746-3750
    • Breslauer, K.J.1
  • 8
    • 0028826669 scopus 로고
    • Trinucleotide models for DNAbending propensity: Comparison of models based on DNaseI digestion and nucleosome packaging data
    • Brukner,I. et al. (1995) Trinucleotide models for DNAbending propensity: Comparison of models based on DNaseI digestion and nucleosome packaging data. J. Biomol. Struct. Dyn., 13, 309-317.
    • (1995) J. Biomol. Struct. Dyn , vol.13 , pp. 309-317
    • Brukner, I.1
  • 9
    • 68549122401 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian promoter architecture and evolution
    • Carninci,P. et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet., 309, 1559-1563.
    • (2006) Nat. Genet , vol.309 , pp. 1559-1563
    • Carninci, P.1
  • 10
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • Davuluri,R.V. et al. (2001) Computational identification of promoters and first exons in the human genome. Nat. Genet., 29 412-417.
    • (2001) Nat. Genet , vol.29 , pp. 412-417
    • Davuluri, R.V.1
  • 11
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12, 458-461.
    • (2002) Genome Res , vol.12 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.2
  • 12
    • 0030003963 scopus 로고    scopus 로고
    • Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
    • ElHassan,M.A. and Calladine,C.R. (1996) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol., 259, 95-103.
    • (1996) J. Mol. Biol , vol.259 , pp. 95-103
    • ElHassan, M.A.1    Calladine, C.R.2
  • 13
    • 22844445585 scopus 로고    scopus 로고
    • Large-scale structural analysis of the core promoter in mammalian and plant genomes
    • Florquin,K. et al. (2005) Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res., 33, 4255-4264.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4255-4264
    • Florquin, K.1
  • 14
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin,A.A. et al. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247 34-48.
    • (1995) J. Mol. Biol , vol.247 , pp. 34-48
    • Gorin, A.A.1
  • 15
    • 40449135396 scopus 로고    scopus 로고
    • Determining promoter location based on DNA structure firstprinciples calculations
    • Goni,J.R. et al. (2007) Determining promoter location based on DNA structure firstprinciples calculations. Genome Biol., 8, R263.
    • (2007) Genome Biol , vol.8
    • Goni, J.R.1
  • 16
    • 0025184633 scopus 로고
    • Polarized electronic spectra of Z-DNAsingle crystals
    • Ho,P.S. et al. (1990) Polarized electronic spectra of Z-DNAsingle crystals. Biopolymers, 30, 151-163.
    • (1990) Biopolymers , vol.30 , pp. 151-163
    • Ho, P.S.1
  • 17
    • 0028612005 scopus 로고
    • The A-form of DNA: In search of the biological role
    • Ivanov,V.I. and Minchenkova,L.E. (1994) The A-form of DNA: In search of the biological role. Mol. Biol., 28, 1258-1271.
    • (1994) Mol. Biol , vol.28 , pp. 1258-1271
    • Ivanov, V.I.1    Minchenkova, L.E.2
  • 18
    • 38549131376 scopus 로고    scopus 로고
    • The UCSC genome browser database: 2008 update
    • Karolchik,D. et al. (2008) The UCSC genome browser database: 2008 update. Nucleic Acids Res., 36, D773-D779.
    • (2008) Nucleic Acids Res , vol.36
    • Karolchik, D.1
  • 19
    • 0033025047 scopus 로고    scopus 로고
    • Promoter2.0: For the recognition of PoIII promoter sequences
    • Knudsen,S. (1999) Promoter2.0: For the recognition of PoIII promoter sequences. Bioinformatics, 15, 356-361.
    • (1999) Bioinformatics , vol.15 , pp. 356-361
    • Knudsen, S.1
  • 20
    • 0012253746 scopus 로고    scopus 로고
    • Computational analysis of core promoters in the Drosophila genome
    • research0087.1-research0087.12
    • Ohler,U. (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol., 3, research0087.1-research0087.12.
    • (2002) Genome Biol , vol.3
    • Ohler, U.1
  • 21
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson,W.K. et al. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA 95, 11163-11168.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1
  • 22
    • 0018143102 scopus 로고
    • Optimized potential function for calculation of nucleic-acid interaction energies. 1. Base stacking
    • Ornstein,R.L. et al. (1978) Optimized potential function for calculation of nucleic-acid interaction energies. 1. Base stacking. Biopolymers, 17, 2341-2360.
    • (1978) Biopolymers , vol.17 , pp. 2341-2360
    • Ornstein, R.L.1
  • 23
    • 0033563512 scopus 로고    scopus 로고
    • The biology of eukaryotic promoter prediction-a review
    • Pedersen,A.G. et al. (1999) The biology of eukaryotic promoter prediction-a review. Comput. Chem., 23, 191-207.
    • (1999) Comput. Chem , vol.23 , pp. 191-207
    • Pedersen, A.G.1
  • 24
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell,S.C. et al. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
    • (1986) J. Mol. Biol , vol.191 , pp. 659-675
    • Satchwell, S.C.1
  • 25
    • 0034737325 scopus 로고    scopus 로고
    • Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach
    • Scherf,M. et al. (2000) Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach. J. Mol. Biol., 297, 599-606.
    • (2000) J. Mol. Biol , vol.297 , pp. 599-606
    • Scherf, M.1
  • 26
    • 0028936684 scopus 로고
    • Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness
    • Sivolob,A.V. and Khrapunov,S.N. (1995) Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness. J. Mol. Biol., 247, 918-931.
    • (1995) J. Mol. Biol , vol.247 , pp. 918-931
    • Sivolob, A.V.1    Khrapunov, S.N.2
  • 27
    • 0042622334 scopus 로고    scopus 로고
    • PromH: Promoters identification using orthologous genomic sequences
    • Solovyev,V.V. and Shahmuradov,I.A. (2003) PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res., 31, 3540-3545.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3540-3545
    • Solovyev, V.V.1    Shahmuradov, I.A.2
  • 28
    • 33748653762 scopus 로고    scopus 로고
    • Automatic annotation of eukaryotic genes, pseudogenes and promoters
    • Solovyev,V. et al. (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol., 7, 11-12.
    • (2006) Genome Biol , vol.7 , pp. 11-12
    • Solovyev, V.1
  • 29
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto,N. et al. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
    • (1996) Nucleic Acids Res , vol.24 , pp. 4501-4505
    • Sugimoto, N.1
  • 30
    • 0347756647 scopus 로고    scopus 로고
    • DBTSS, DataBase of Transcriptional Start Sites: Progress report
    • Suzuki,Y. et al. (2004) DBTSS, DataBase of Transcriptional Start Sites: Progress report. Nucleic Acids Res., 32, D78-D81.
    • (2004) Nucleic Acids Res , vol.32
    • Suzuki, Y.1
  • 31
    • 33747881750 scopus 로고    scopus 로고
    • The general transcription machinery and general cofactors
    • Thomas,M.C. and Chiang,C.M. (2006) The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol., 41, 105-178.
    • (2006) Crit. Rev. Biochem. Mol. Biol , vol.41 , pp. 105-178
    • Thomas, M.C.1    Chiang, C.M.2
  • 33
    • 2442684104 scopus 로고    scopus 로고
    • An evaluation of new criteria for CpG islands in the human genome as gene markers
    • Yong,W. et al. (2004) An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics, 20 1170-1177.
    • (2004) Bioinformatics , vol.20 , pp. 1170-1177
    • Yong, W.1
  • 34
    • 34447525636 scopus 로고    scopus 로고
    • Boosting with stumps for predicting transcription start sites
    • Zhao,X. et al. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol., 8, R17.
    • (2007) Genome Biol , vol.8
    • Zhao, X.1


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