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Volumn 22, Issue 1, 2007, Pages 49-69

Using a VOM model for reconstructing potential coding regions in EST sequences

Author keywords

Coding and noncoding DNA; Context tree; Gene annotation; Sequencing error detection and correction; Variable order Markov model

Indexed keywords


EID: 34247160350     PISSN: 09434062     EISSN: 16139658     Source Type: Journal    
DOI: 10.1007/s00180-007-0021-8     Document Type: Article
Times cited : (17)

References (35)
  • 1
    • 27344458404 scopus 로고    scopus 로고
    • On prediction using variable order markov models
    • Begleiter R, El-Yaniv R, Yona G (2004) On prediction using variable order markov models. J Artif Intell 22:385-421
    • (2004) J Artif Intell , vol.22 , pp. 385-421
    • Begleiter, R.1    El-Yaniv, R.2    Yona, G.3
  • 2
    • 0035109647 scopus 로고    scopus 로고
    • Variations on probabilistic suffix trees: Statistical modeling and prediction of protein families
    • Bejerano G (2001) Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bioinformatics 17(1):23-43
    • (2001) Bioinformatics , vol.17 , Issue.1 , pp. 23-43
    • Bejerano, G.1
  • 3
    • 0344667562 scopus 로고    scopus 로고
    • CSPC: A monitoring procedure for state dependent processes
    • Ben-Gal I, Shmilovici A, Morag G (2003) CSPC: a monitoring procedure for state dependent processes. Technometrics 45(4):293-311
    • (2003) Technometrics , vol.45 , Issue.4 , pp. 293-311
    • Ben-Gal, I.1    Shmilovici, A.2    Morag, G.3
  • 4
    • 20744440509 scopus 로고    scopus 로고
    • Identification of transcription factor binding sites with variable-order Bayesian networks
    • Ben-Gal I, Shani A et al. (2005) Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics 21(11):2657-2666
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2657-2666
    • Ben-Gal, I.1    Shani, A.2
  • 5
    • 0034238085 scopus 로고    scopus 로고
    • finding borders between coding and noncoding DNA regions by an entropic segmentation method
    • Bernaola-Galvan P, Grosse I et al. (2000) finding borders between coding and noncoding DNA regions by an entropic segmentation method. Phys Rev Lett 85(6):1342-1345
    • (2000) Phys Rev Lett , vol.85 , Issue.6 , pp. 1342-1345
    • Bernaola-Galvan, P.1    Grosse, I.2
  • 7
    • 29144445262 scopus 로고    scopus 로고
    • ExonHunter: A comprehensive approach to gene finding
    • Brejova B, Brown D.G, Li M, Vinai T (2005) ExonHunter: a comprehensive approach to gene finding. Bioinformatics 21(Suppl 1):i57-i65
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Brejova, B.1    Brown, D.G.2    Li, M.3    Vinai, T.4
  • 8
    • 0031872701 scopus 로고    scopus 로고
    • Frame: Detection of genomic sequencing errors
    • Brown NP, Sander C et al. (1998) Frame: detection of genomic sequencing errors. Bioinformatics 14(4):367-371.
    • (1998) Bioinformatics , vol.14 , Issue.4 , pp. 367-371
    • Brown, N.P.1    Sander, C.2
  • 9
    • 0032104509 scopus 로고    scopus 로고
    • Finding the genes in genomic DNA
    • Burge C, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8(3):346-354
    • (1998) Curr Opin Struct Biol , vol.8 , Issue.3 , pp. 346-354
    • Burge, C.1    Karlin, S.2
  • 10
    • 85142165229 scopus 로고    scopus 로고
    • Cawley SL, Pachter L (2003) HMM sampling and applications to gene finding and alternative splicing. Bioinformatics 19(Suppl 2):ii36-ii41
    • Cawley SL, Pachter L (2003) HMM sampling and applications to gene finding and alternative splicing. Bioinformatics 19(Suppl 2):ii36-ii41
  • 12
    • 0028273691 scopus 로고
    • Relations between entropy and error probability
    • Feder M, Merhav N (1994) Relations between entropy and error probability. IEEE Trans Inf Theory 40(1):259-266
    • (1994) IEEE Trans Inf Theory , vol.40 , Issue.1 , pp. 259-266
    • Feder, M.1    Merhav, N.2
  • 13
    • 0030218799 scopus 로고    scopus 로고
    • Finding genes by computer: The state of the art
    • Fickett JW (1996) Finding genes by computer: the state of the art. Trends Genet 12(8):316-320
    • (1996) Trends Genet , vol.12 , Issue.8 , pp. 316-320
    • Fickett, J.W.1
  • 14
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett JW, Tung CS (1992) Assessment of protein coding measures. Nucl Acids Res 20(24): 6441-6450
    • (1992) Nucl Acids Res , vol.20 , Issue.24 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.S.2
  • 15
    • 0031211090 scopus 로고    scopus 로고
    • A decision theoretic generalization of on-line learning and an application to boosting
    • Freund Y, Schapira RE (1997) A decision theoretic generalization of on-line learning and an application to boosting. J Comput Syst Sci 55(1):119-139
    • (1997) J Comput Syst Sci , vol.55 , Issue.1 , pp. 119-139
    • Freund, Y.1    Schapira, R.E.2
  • 16
    • 34247111033 scopus 로고    scopus 로고
    • GENIE data-sets, from Genbank version 105 (1998) Available: http://www.fruitfly.org/seq_tools/datasets/Human/CDS_v105/;http://www.fruitfly. org/seq_tools/datasets/Human/intron_v105/
    • GENIE data-sets, from Genbank version 105 (1998) Available: http://www.fruitfly.org/seq_tools/datasets/Human/CDS_v105/;http://www.fruitfly. org/seq_tools/datasets/Human/intron_v105/
  • 17
    • 0038014879 scopus 로고    scopus 로고
    • Co-clustering of biological networks and gene expression data
    • Hanisch D et al. (2002) Co-clustering of biological networks and gene expression data. Bioinformatics 1:1-10
    • (2002) Bioinformatics , vol.1 , pp. 1-10
    • Hanisch, D.1
  • 19
    • 0001818891 scopus 로고
    • Measuring correlations in symbols sequences
    • Herzel H, Grosse I (1995) Measuring correlations in symbols sequences. Phys A 216:518-542
    • (1995) Phys A , vol.216 , pp. 518-542
    • Herzel, H.1    Grosse, I.2
  • 20
    • 0033290515 scopus 로고    scopus 로고
    • ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
    • AAAI Press, Menlo Park
    • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceedings of intelligent systems for molecular biology. AAAI Press, Menlo Park
    • (1999) Proceedings of intelligent systems for molecular biology
    • Iseli, C.1    Jongeneel, C.V.2    Bucher, P.3
  • 21
    • 0041853625 scopus 로고    scopus 로고
    • MATCH: A tool for searching transcription factor binding sites in DNA sequences
    • Kel AE, Gossling E et al. (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucl Acids Res 31 (13):3576-3579
    • (2003) Nucl Acids Res , vol.31 , Issue.13 , pp. 3576-3579
    • Kel, A.E.1    Gossling, E.2
  • 22
    • 0642307369 scopus 로고    scopus 로고
    • EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance
    • Available Online
    • Larsen TS, Krogh A (2003) EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinf 4(21) Available Online www.biomedcentral.com/1471-2105/4/21
    • (2003) BMC Bioinf , vol.4 , Issue.21
    • Larsen, T.S.1    Krogh, A.2
  • 23
    • 85142155387 scopus 로고    scopus 로고
    • Lottaz C, Iseli C, Jongeneel CV, Bucher P (2003) Modeling sequencing errors by combining Hidden markov models. Bioinformatics 19(Suppl 2):ii103-ii112
    • Lottaz C, Iseli C, Jongeneel CV, Bucher P (2003) Modeling sequencing errors by combining Hidden markov models. Bioinformatics 19(Suppl 2):ii103-ii112
  • 24
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders
    • Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatic 20:2878-2879
    • (2004) Bioinformatic , vol.20 , pp. 2878-2879
    • Majoros, W.H.1    Pertea, M.2    Salzberg, S.L.3
  • 26
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 17:56-60
    • (2001) Trends Genet , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 27
    • 0033030389 scopus 로고    scopus 로고
    • Interpolated Markov chains for eukaryotic promoter recognition
    • Ohler U, Harbeck S, Niemann H, Noth E, Reese M (1999) Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 15(5):362-369
    • (1999) Bioinformatics , vol.15 , Issue.5 , pp. 362-369
    • Ohler, U.1    Harbeck, S.2    Niemann, H.3    Noth, E.4    Reese, M.5
  • 29
    • 0020824731 scopus 로고
    • A universal data compression system
    • Rissanen J (1983) A universal data compression system. IEEE Trans Inf Theory 29(5):656-664
    • (1983) IEEE Trans Inf Theory , vol.29 , Issue.5 , pp. 656-664
    • Rissanen, J.1
  • 30
    • 34247133227 scopus 로고    scopus 로고
    • Using a compressibility measure to distinguish coding and noncoding DNA
    • Stat
    • Shmilovici A, Ben-Gal I (2004) Using a compressibility measure to distinguish coding and noncoding DNA. Far East J Theoret Stat 13(2):215-234
    • (2004) Far East J Theoret , vol.13 , Issue.2 , pp. 215-234
    • Shmilovici, A.1    Ben-Gal, I.2
  • 31
    • 84867924938 scopus 로고    scopus 로고
    • Using a stochastic complexity measure to check the efficient market hypothesis
    • Shmilovici A, Alon-Brimer Y, Hauser S (2003) Using a stochastic complexity measure to check the efficient market hypothesis. Comput Econ 22(3):273-284
    • (2003) Comput Econ , vol.22 , Issue.3 , pp. 273-284
    • Shmilovici, A.1    Alon-Brimer, Y.2    Hauser, S.3
  • 32
    • 0035397419 scopus 로고    scopus 로고
    • Adaptive context trees and text clustering
    • Vert JP (2001) Adaptive context trees and text clustering. IEEE Trans Inf Theory 47(5):1884-1901
    • (2001) IEEE Trans Inf Theory , vol.47 , Issue.5 , pp. 1884-1901
    • Vert, J.P.1
  • 33
    • 0029075793 scopus 로고
    • Correcting sequencing errors in DNA coding regions using a dynamic programming approach
    • Xu Y, Mural RJ, Uberbacher EC (1995) Correcting sequencing errors in DNA coding regions using a dynamic programming approach. Bioinformatics 11:117-124
    • (1995) Bioinformatics , vol.11 , pp. 117-124
    • Xu, Y.1    Mural, R.J.2    Uberbacher, E.C.3
  • 35
    • 0035333761 scopus 로고    scopus 로고
    • A universal prediction lemma and applications to universal data compression and prediction
    • Ziv J (2001) A universal prediction lemma and applications to universal data compression and prediction. IEEE Trans Inf Theory 47(4):1528-1532
    • (2001) IEEE Trans Inf Theory , vol.47 , Issue.4 , pp. 1528-1532
    • Ziv, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.