메뉴 건너뛰기




Volumn 46, Issue 1, 2006, Pages 78-85

A physicochemical model for analyzing DNA sequences

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; GENES; HYDROGEN BONDS; MATHEMATICAL MODELS; PROTEINS; VECTORS;

EID: 33244465205     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050119x     Document Type: Conference Paper
Times cited : (20)

References (47)
  • 1
    • 0000241874 scopus 로고
    • GENMARK: Parallel gene recognition for both DNA strands
    • Bordovsky, M. Y.; McIninch, J. D. GENMARK: Parallel gene recognition for both DNA strands. Comput. Chem. 1993, 17, 123-133.
    • (1993) Comput. Chem. , vol.17 , pp. 123-133
    • Bordovsky, M.Y.1    McIninch, J.D.2
  • 2
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hrnm: New solutions for gene finding
    • Lukashin, A. V.; Bordovsky, M. GeneMark.hrnm: new solutions for gene finding. Nucleic Acids Res. 1998, 26, 1107-1115.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Bordovsky, M.2
  • 4
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C.; Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol. 1997, 268 (1), 78-94.
    • (1997) J. Mol. Biol. , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 5
    • 0027944605 scopus 로고
    • A hidden Markov model that finds genes in E. coli DNA
    • Krogh, A.; Mian, I. S.; Haussler, D. A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res. 1994, 22, 4768-4778.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4768-4778
    • Krogh, A.1    Mian, I.S.2    Haussler, D.3
  • 7
    • 0036772510 scopus 로고    scopus 로고
    • Comparative ab initio prediction of gene structures using pair HMMs
    • Meyer, I. M.; Durbin, R. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 2002, 18, 1309-1318.
    • (2002) Bioinformatics , vol.18 , pp. 1309-1318
    • Meyer, I.M.1    Durbin, R.2
  • 8
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • Salzberg, S. L.; Deicher, A. L.; Kasif, S.; White, O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998, 26, 544-548.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 544-548
    • Salzberg, S.L.1    Deicher, A.L.2    Kasif, S.3    White, O.4
  • 9
    • 0030810993 scopus 로고    scopus 로고
    • Finding genes in DNA with a Hidden Markov Model
    • Henderson, J.; Salzberg, S.; Fasman, K. H. Finding genes in DNA with a Hidden Markov Model. J. Comput. Biol. 1997, 4, 127-141.
    • (1997) J. Comput. Biol. , vol.4 , pp. 127-141
    • Henderson, J.1    Salzberg, S.2    Fasman, K.H.3
  • 11
    • 0036166511 scopus 로고    scopus 로고
    • Locating probable genes using Fourier transform approach
    • Issac, B.; Singh, H.; Kaur, H.; Raghava, G. P. Locating probable genes using Fourier transform approach. Bioinformatics 2002, 18, 196-197.
    • (2002) Bioinformatics , vol.18 , pp. 196-197
    • Issac, B.1    Singh, H.2    Kaur, H.3    Raghava, G.P.4
  • 12
    • 0027229632 scopus 로고
    • Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural networks
    • Snyder, E. E.; Stormo, G. D. Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res. 1993, 21, 607-613.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 607-613
    • Snyder, E.E.1    Stormo, G.D.2
  • 14
    • 0029955046 scopus 로고    scopus 로고
    • Gene structure prediction using information on homologous protein sequence
    • Rogozin, I. B.; Milanesi, L.; Kolchanov, N. A. Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci. 1996, 12, 161-170.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 161-170
    • Rogozin, I.B.1    Milanesi, L.2    Kolchanov, N.A.3
  • 15
    • 0034129662 scopus 로고    scopus 로고
    • Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (Iron) and improved accuracy by allowing for long gaps
    • Gotoh, O. Homology-based gene structure prediction: simplified matching algorithm using a translated codon (Iron) and improved accuracy by allowing for long gaps. Bioinformatics 2000, 16, 190-202.
    • (2000) Bioinformatics , vol.16 , pp. 190-202
    • Gotoh, O.1
  • 16
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • Kan, Z.; Rouchka, E. C.; Gish, W. R.; States, D. J. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 2001, 11, 889-900.
    • (2001) Genome Res. , vol.11 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 17
    • 0036455972 scopus 로고    scopus 로고
    • AGenDA: Gene prediction by comparative sequence analysis
    • Rinner, O.; Morgenstern, B. AGenDA: gene prediction by comparative sequence analysis. In Silico Biol. 2002, 2, 195-205.
    • (2002) In Silico Biol. , vol.2 , pp. 195-205
    • Rinner, O.1    Morgenstern, B.2
  • 18
    • 0041589538 scopus 로고    scopus 로고
    • EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences
    • Foissac, S.; Bardou, P.; Moisan, A.; Cros, M. J.; Schiex, T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res. 2003, 31, 3742-3745.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3742-3745
    • Foissac, S.1    Bardou, P.2    Moisan, A.3    Cros, M.J.4    Schiex, T.5
  • 19
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf, I.; Flicek, P.; Duan, D.; Brent, M. R. Integrating genomic homology into gene structure prediction. Bioinformatics 2001, 17, S140-S148.
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 20
    • 0029173791 scopus 로고
    • Identification of human gene structure using linear discriminant functions and dynamic programming
    • Solovyev, V. V.; Salamov, A. A.; Lawrence, C. B. Identification of human gene structure using linear discriminant functions and dynamic programming. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1995, 3, 367-375.
    • (1995) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.3 , pp. 367-375
    • Solovyev, V.V.1    Salamov, A.A.2    Lawrence, C.B.3
  • 21
    • 0032526384 scopus 로고    scopus 로고
    • Pombe: A gene-finding and exon-intron structure prediction system for fission yeast
    • Chen, T.; Zhang, M. Q. Pombe: a gene-finding and exon-intron structure prediction system for fission yeast. Yeast 1998, 14, 701-710.
    • (1998) Yeast , vol.14 , pp. 701-710
    • Chen, T.1    Zhang, M.Q.2
  • 22
    • 0033384536 scopus 로고    scopus 로고
    • Finding prokaryotic genes by the 'frame-by-frame' algorithm: Targeting gene starts and overlapping genes
    • Shmatkov, A. M.; Melikyan, A. A.; Chernousko, F. L.; Bordovsky, M. Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. Bioinformatics 1999, 15, 874-886.
    • (1999) Bioinformatics , vol.15 , pp. 874-886
    • Shmatkov, A.M.1    Melikyan, A.A.2    Chernousko, F.L.3    Bordovsky, M.4
  • 23
    • 0036171256 scopus 로고    scopus 로고
    • Physics-based gene identification: Proof of concept for Plasmodium falciparum
    • Yeramian, E.; Bonnefoy, S.; Langsley, G. Physics-based gene identification: proof of concept for Plasmodium falciparum. Bioinformatics 2002, 18, 190-193.
    • (2002) Bioinformatics , vol.18 , pp. 190-193
    • Yeramian, E.1    Bonnefoy, S.2    Langsley, G.3
  • 24
    • 0036679565 scopus 로고    scopus 로고
    • Improving gene recognition accuracy by combining predictions from two gene-finding programs
    • Rogic, S.; Ouellette, B. F.; Mackworth, A. K. Improving gene recognition accuracy by combining predictions from two gene-finding programs. Bioinformatics 2002, 18, 1034-1045.
    • (2002) Bioinformatics , vol.18 , pp. 1034-1045
    • Rogic, S.1    Ouellette, B.F.2    Mackworth, A.K.3
  • 25
    • 0037444091 scopus 로고    scopus 로고
    • ZCURVE: A new system for recognizing protein-coding genes in bacterial and archaeal genomes
    • Guo, F. B.; Ou, H. Y.; Zhang, C. T. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 2003, 31, 1780-1789.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1780-1789
    • Guo, F.B.1    Ou, H.Y.2    Zhang, C.T.3
  • 26
    • 0036280536 scopus 로고    scopus 로고
    • Evaluation of gene-finding algorithms by a content-balancing accuracy index
    • Zhang, C. T.; Zhang, R. Evaluation of gene-finding algorithms by a content-balancing accuracy index. J. Biomol. Struct. Dyn. 2002, 19, 1045-1052.
    • (2002) J. Biomol. Struct. Dyn. , vol.19 , pp. 1045-1052
    • Zhang, C.T.1    Zhang, R.2
  • 27
    • 0036796369 scopus 로고    scopus 로고
    • Current methods of gene prediction, their strengths and weaknesses
    • Mathe, C.; Sagot, M. F.; Schiex, T.; Rouze, P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 2002, 30, 4103-4117.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4103-4117
    • Mathe, C.1    Sagot, M.F.2    Schiex, T.3    Rouze, P.4
  • 28
    • 0035002807 scopus 로고    scopus 로고
    • Evaluation of genefinding programs on mammalian sequences
    • Rogic, S.; Mackworth, A. K.; Ouellette, F. B. Evaluation of genefinding programs on mammalian sequences. Genome Res. 2001, 11, 817-832.
    • (2001) Genome Res. , vol.11 , pp. 817-832
    • Rogic, S.1    Mackworth, A.K.2    Ouellette, F.B.3
  • 29
    • 33244494151 scopus 로고    scopus 로고
    • a dissertation submitted to Indian Institute of Technology, Delhi, India, in partial fulfilment of the requirement for the degree of five-year integrated Master of Technology in Biochemical Engineering & Biotechnology
    • Kritee. Towards a chemical model to predict genes & analyze prokaryotic genomes; a dissertation submitted to Indian Institute of Technology, Delhi, India, in partial fulfilment of the requirement for the degree of five-year integrated Master of Technology in Biochemical Engineering & Biotechnology, 2001.
    • (2001) Towards a Chemical Model to Predict Genes & Analyze Prokaryotic Genomes
    • Kritee1
  • 30
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • and references therein
    • Honig, B. H.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149 and references therein.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.H.1    Nicholls, A.2
  • 31
    • 0031451044 scopus 로고    scopus 로고
    • Beyond the Wobble: The rule of conjugates
    • Jayaram, B. Beyond the Wobble: The rule of conjugates. J. Mol. Evol. 1997, 45, 704-705.
    • (1997) J. Mol. Evol. , vol.45 , pp. 704-705
    • Jayaram, B.1
  • 32
    • 33244482992 scopus 로고    scopus 로고
    • A dissertation submitted to Indian Institute of Technology, Delhi, in partial fulfilment of the requirement for the degree of Master of Science in Chemistry
    • Khurana, E. Chemical Model for Genome Analysis. A dissertation submitted to Indian Institute of Technology, Delhi, in partial fulfilment of the requirement for the degree of Master of Science in Chemistry, 2002.
    • (2002) Chemical Model for Genome Analysis
    • Khurana, E.1
  • 35
    • 33244471482 scopus 로고    scopus 로고
    • Reference deleted in press
    • Reference deleted in press.
  • 38
    • 0025449027 scopus 로고
    • Perceptron-based learning algorithm
    • Gallant, S. I. Perceptron-Based Learning Algorithm. IEEE Trans. Neural Networks 1990, 2 (1), 179-191.
    • (1990) IEEE Trans. Neural Networks , vol.2 , Issue.1 , pp. 179-191
    • Gallant, S.I.1
  • 40
    • 33244496133 scopus 로고    scopus 로고
    • ftp://ftp.ncbi.nih.gov/genomes/Bacteria/.
  • 41
    • 33244480049 scopus 로고    scopus 로고
    • Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY
    • (41 ) David, W. Mount Sequence and Genome Analysis; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2001; p 357.
    • (2001) Mount Sequence and Genome Analysis , pp. 357
    • David, W.1
  • 42
    • 2142859937 scopus 로고    scopus 로고
    • Re-annotation of genome microbial CoDing-Sequences: Finding new genes and inaccurately annotated genes
    • Bocs, S.; Danchin, A.; Medigue, C. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes. BMC BioInformatics 2002, 3, 5.
    • (2002) BMC BioInformatics , vol.3 , pp. 5
    • Bocs, S.1    Danchin, A.2    Medigue, C.3
  • 43
    • 4344568000 scopus 로고    scopus 로고
    • Genome Update: Annotation quality in sequenced microbial genomes
    • Ussery, D. W.; Hallin, P. F. Genome Update: annotation quality in sequenced microbial genomes. Microbiology 2004, 150, 2015-2017.
    • (2004) Microbiology , vol.150 , pp. 2015-2017
    • Ussery, D.W.1    Hallin, P.F.2
  • 44
    • 0038381548 scopus 로고    scopus 로고
    • An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data
    • Kanhere, A.; Bansal, M. An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data. Nucleic Acids Res. 2003, 31, 2647-2658.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2647-2658
    • Kanhere, A.1    Bansal, M.2
  • 45
    • 0033884290 scopus 로고    scopus 로고
    • Optimization of nucleic acid sequences
    • Lafontaine, I.; Lavery, R. Optimization of Nucleic Acid Sequences. Biophys. J. 2000, 79, 680-685.
    • (2000) Biophys. J. , vol.79 , pp. 680-685
    • Lafontaine, I.1    Lavery, R.2
  • 46
    • 33244461895 scopus 로고    scopus 로고
    • Molecular dynamics simulations of DNA curvature, flexibility, dynamical aspects of helix phasing and premelting phenomena
    • in press
    • Beveridge, D. L.; Dixit, S. B.; Barreiro, G.; Thayer, K. M. Molecular Dynamics Simulations of DNA Curvature, Flexibility, Dynamical Aspects of Helix Phasing and Premelting Phenomena. Biopolymers NAS 2005, in press.
    • (2005) Biopolymers NAS
    • Beveridge, D.L.1    Dixit, S.B.2    Barreiro, G.3    Thayer, K.M.4
  • 47
    • 13744259639 scopus 로고    scopus 로고
    • Quantitative evaluation of protein-DNA interactions using an optimized knowledge potential
    • Liu, Z.; Mao, F.; Guo bo Yan, J.-t.; Wang, P.; Qu, Y.; Xu, Y. Quantitative evaluation of protein-DNA interactions using an optimized knowledge potential. Nucleic Acids Res. 2005, 33 (2), 546-548.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.2 , pp. 546-548
    • Liu, Z.1    Mao, F.2    Guo Bo Yan, J.-T.3    Wang, P.4    Qu, Y.5    Xu, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.