메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Exploration of multivariate analysis in microbial coding sequence modeling

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION RESULTS; CODING SEQUENCES; GENE FINDING; GENOMIC DNA; MARKOV MODEL; MULTI VARIATE ANALYSIS; MULTIVARIATE METHODS; OVERLAPPING GENES; PARTIAL LEAST SQUARE (PLS); PROMOTER REGION; PROTEIN SEQUENCES;

EID: 84860817731     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-97     Document Type: Article
Times cited : (7)

References (43)
  • 1
    • 44649172475 scopus 로고    scopus 로고
    • How much non-coding DNA do eukaryotes require?
    • 10.1016/j.jtbi.2008.02.005, 18384817
    • Ahnert S, Fink T, Zinovyev A. How much non-coding DNA do eukaryotes require?. J Theor Biol 2008, 252(4):587-592. 10.1016/j.jtbi.2008.02.005, 18384817.
    • (2008) J Theor Biol , vol.252 , Issue.4 , pp. 587-592
    • Ahnert, S.1    Fink, T.2    Zinovyev, A.3
  • 2
    • 32044474423 scopus 로고    scopus 로고
    • Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
    • 1361709, 16365377
    • Toh H, Weiss B, Perkin S, Yamashita A, Oshima K, Hattori M, Aksoy S. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 2006, 16(2):149-156. 1361709, 16365377.
    • (2006) Genome Res , vol.16 , Issue.2 , pp. 149-156
    • Toh, H.1    Weiss, B.2    Perkin, S.3    Yamashita, A.4    Oshima, K.5    Hattori, M.6    Aksoy, S.7
  • 3
    • 33745775924 scopus 로고    scopus 로고
    • Computational approaches to gene prediction
    • Do J, Choi D. Computational approaches to gene prediction. J Microbiol Seoul 2006, 44(2):137.
    • (2006) J Microbiol Seoul , vol.44 , Issue.2 , pp. 137
    • Do, J.1    Choi, D.2
  • 4
    • 77949482581 scopus 로고    scopus 로고
    • Missing genes in the annotation of prokaryotic genomes
    • Warren A, Archuleta J, Feng W, Setubal J. Missing genes in the annotation of prokaryotic genomes. BMC Bioinf 2010, 11:131.
    • (2010) BMC Bioinf , vol.11 , pp. 131
    • Warren, A.1    Archuleta, J.2    Feng, W.3    Setubal, J.4
  • 6
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • 10.1093/bioinformatics/btm009, 2387122, 17237039
    • Delcher A, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 673-679
    • Delcher, A.1    Bratke, K.2    Powers, E.3    Salzberg, S.4
  • 7
    • 0642307369 scopus 로고    scopus 로고
    • EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance
    • 10.1186/1471-2105-4-21, 521197, 12783628
    • Larsen T, Krogh A. EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance. BMC bioinformatics 2003, 4:21. 10.1186/1471-2105-4-21, 521197, 12783628.
    • (2003) BMC bioinformatics , vol.4 , pp. 21
    • Larsen, T.1    Krogh, A.2
  • 10
    • 0027208707 scopus 로고
    • Recognition of genes in DNA sequence with ambiguities
    • 10.1016/0303-2647(93)90068-N, 8374073
    • Borodovsky M, McIninch J. Recognition of genes in DNA sequence with ambiguities. Biosystems 1993, 30(1-3):161-171. 10.1016/0303-2647(93)90068-N, 8374073.
    • (1993) Biosystems , vol.30 , Issue.1-3 , pp. 161-171
    • Borodovsky, M.1    McIninch, J.2
  • 11
    • 0000241874 scopus 로고
    • GENMARK: parallel gene recognition for both DNA strands
    • Borodovsky M, McIninch J. GENMARK: parallel gene recognition for both DNA strands. Comput Chem 1993, 17(2):123-133.
    • (1993) Comput Chem , vol.17 , Issue.2 , pp. 123-133
    • Borodovsky, M.1    McIninch, J.2
  • 12
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: new solutions for gene finding
    • 10.1093/nar/26.4.1107, 147337, 9461475
    • Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucl Acids Res 1998, 26:1107-1115. 10.1093/nar/26.4.1107, 147337, 9461475.
    • (1998) Nucl Acids Res , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 13
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • 10.1093/nar/26.2.544, 147303, 9421513
    • Salzberg S, Delcher A, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucl Acids Res 1998, 26(2):544. 10.1093/nar/26.2.544, 147303, 9421513.
    • (1998) Nucl Acids Res , vol.26 , Issue.2 , pp. 544
    • Salzberg, S.1    Delcher, A.2    Kasif, S.3    White, O.4
  • 14
    • 0043123003 scopus 로고    scopus 로고
    • AMIGene: annotation of microbial genes
    • 10.1093/nar/gkg590, 168996, 12824403
    • Bocs S, Cruveiller S, Vallenet D, Nuel G, Médigue C. AMIGene: annotation of microbial genes. Nucl Acids Res 2003, 31(13):3723. 10.1093/nar/gkg590, 168996, 12824403.
    • (2003) Nucl Acids Res , vol.31 , Issue.13 , pp. 3723
    • Bocs, S.1    Cruveiller, S.2    Vallenet, D.3    Nuel, G.4    Médigue, C.5
  • 15
    • 0642307369 scopus 로고    scopus 로고
    • EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance
    • Larsen TS, Krogh A. EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinf 2003, 4:21.
    • (2003) BMC Bioinf , vol.4 , pp. 21
    • Larsen, T.S.1    Krogh, A.2
  • 16
    • 16644401595 scopus 로고    scopus 로고
    • Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory
    • Azad R, Borodovsky M. Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Briefings Bioinf 2004, 5(2):118-130.
    • (2004) Briefings Bioinf , vol.5 , Issue.2 , pp. 118-130
    • Azad, R.1    Borodovsky, M.2
  • 20
    • 40449093894 scopus 로고    scopus 로고
    • Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
    • 10.1186/gb-2007-8-12-r267, 2246269, 18088402
    • Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 2007, 8:R267. 10.1186/gb-2007-8-12-r267, 2246269, 18088402.
    • (2007) Genome Biol , vol.8
    • Willenbrock, H.1    Hallin, P.F.2    Wassenaar, T.M.3    Ussery, D.W.4
  • 21
    • 59949090259 scopus 로고    scopus 로고
    • De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
    • 2652211, 19015323
    • Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 2009, 19:294-305. 2652211, 19015323.
    • (2009) Genome Res , vol.19 , pp. 294-305
    • Reinhardt, J.A.1    Baltrus, D.A.2    Nishimura, M.T.3    Jeck, W.R.4    Jones, C.D.5    Dangl, J.L.6
  • 22
    • 70349588017 scopus 로고    scopus 로고
    • Canonical partial least squares a unified PLS approach to classification and regression problems
    • Indahl U, Liland K, Næs T. Canonical partial least squares a unified PLS approach to classification and regression problems. J Chemom 2009, 23(9):495-504.
    • (2009) J Chemom , vol.23 , Issue.9 , pp. 495-504
    • Indahl, U.1    Liland, K.2    Næs, T.3
  • 23
    • 0036083139 scopus 로고    scopus 로고
    • Orthogonal projections to latent structures (O-PLS)
    • Trygg J, Wold S. Orthogonal projections to latent structures (O-PLS). J Chemom 2002, 16(3):119-128.
    • (2002) J Chemom , vol.16 , Issue.3 , pp. 119-128
    • Trygg, J.1    Wold, S.2
  • 24
    • 34147174475 scopus 로고    scopus 로고
    • MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
    • Zhu H, Hu GQ, Yang YF, Wang J, She ZS. MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. BMC Bioinf 2007, 8:97.
    • (2007) BMC Bioinf , vol.8 , pp. 97
    • Zhu, H.1    Hu, G.Q.2    Yang, Y.F.3    Wang, J.4    She, Z.S.5
  • 26
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: current status, policy and new initiatives
    • 2686572, 18927115
    • Pruitt K, Tatusova T, Klimke W, Maglott D. NCBI Reference Sequences: current status, policy and new initiatives. Nucl Acids Res 2009, 37(suppl 1):D32-D36. 2686572, 18927115.
    • (2009) Nucl Acids Res , vol.37 , Issue.SUPPL. 1
    • Pruitt, K.1    Tatusova, T.2    Klimke, W.3    Maglott, D.4
  • 27
    • 0034053725 scopus 로고    scopus 로고
    • A greedy algorithm for aligning DNA sequences
    • 10.1089/10665270050081478, 10890397
    • Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7(1-2):203-214. 10.1089/10665270050081478, 10890397.
    • (2000) J Comput Biol , vol.7 , Issue.1-2 , pp. 203-214
    • Zhang, Z.1    Schwartz, S.2    Wagner, L.3    Miller, W.4
  • 28
    • 4043165754 scopus 로고    scopus 로고
    • Multivariate entropy distance method for prokaryotic gene identification
    • Ouyang Z, Zhu H, Wang J, She Z. Multivariate entropy distance method for prokaryotic gene identification. J Bioinf Comput Biol 2004, 2(2):353-374.
    • (2004) J Bioinf Comput Biol , vol.2 , Issue.2 , pp. 353-374
    • Ouyang, Z.1    Zhu, H.2    Wang, J.3    She, Z.4
  • 29
    • 77952299299 scopus 로고    scopus 로고
    • Reconstructing genome trees of prokaryotes using overlapping genes
    • Chih-Hsien C, Chung-Han Y, Hsien-Tai C, Lung L. Reconstructing genome trees of prokaryotes using overlapping genes. BMC Bioinf 2010, 11:102.
    • (2010) BMC Bioinf , vol.11 , pp. 102
    • Chih-Hsien, C.1    Chung-Han, Y.2    Hsien-Tai, C.3    Lung, L.4
  • 30
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • 10.1093/nar/15.3.1281, 340524, 3547335
    • Sharp P, Li W. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucl Acids Res 1987, 15(3):1281. 10.1093/nar/15.3.1281, 340524, 3547335.
    • (1987) Nucl Acids Res , vol.15 , Issue.3 , pp. 1281
    • Sharp, P.1    Li, W.2
  • 31
    • 0039530516 scopus 로고    scopus 로고
    • Variable length Markov chains
    • Bählmann P, Wyner A. Variable length Markov chains. Ann Stat 1999, 27(2):480-513.
    • (1999) Ann Stat , vol.27 , Issue.2 , pp. 480-513
    • Bählmann, P.1    Wyner, A.2
  • 32
    • 0033030389 scopus 로고    scopus 로고
    • Interpolated markov chains for eukaryotic promoter recognition
    • 10.1093/bioinformatics/15.5.362, 10366656
    • Ohler U, Harbeck S, Niemann H. Interpolated markov chains for eukaryotic promoter recognition. Bioinformatics 1999, 15(5):362. 10.1093/bioinformatics/15.5.362, 10366656.
    • (1999) Bioinformatics , vol.15 , Issue.5 , pp. 362
    • Ohler, U.1    Harbeck, S.2    Niemann, H.3
  • 33
    • 0035973555 scopus 로고    scopus 로고
    • A novel bacterial gene-finding system with improved accuracy in locating start codons
    • 10.1093/dnares/8.3.97, 11475327
    • Yada T, Totoki Y, Takagi T, Nakai K. A novel bacterial gene-finding system with improved accuracy in locating start codons. DNA Res 2001, 8(3):97-106. 10.1093/dnares/8.3.97, 11475327.
    • (2001) DNA Res , vol.8 , Issue.3 , pp. 97-106
    • Yada, T.1    Totoki, Y.2    Takagi, T.3    Nakai, K.4
  • 36
    • 79951493901 scopus 로고    scopus 로고
    • LEEways: tales of EPEC, ATEC and EHEC
    • 10.1111/j.1462-5822.2010.01518.x, 20716205
    • Schmidt M. LEEways: tales of EPEC, ATEC and EHEC. Cell Microbiol 2010, 12(11):1544-1552. 10.1111/j.1462-5822.2010.01518.x, 20716205.
    • (2010) Cell Microbiol , vol.12 , Issue.11 , pp. 1544-1552
    • Schmidt, M.1
  • 37
    • 18244379036 scopus 로고    scopus 로고
    • Horizontal transfer of the high pathogenicity island of Yersinia pseudotuberculosis
    • 10.1128/JB.187.10.3352-3358.2005, 1112006, 15866919
    • Lesic B, Carniel E. Horizontal transfer of the high pathogenicity island of Yersinia pseudotuberculosis. J Bacteriol 2005, 187(10):3352. 10.1128/JB.187.10.3352-3358.2005, 1112006, 15866919.
    • (2005) J Bacteriol , vol.187 , Issue.10 , pp. 3352
    • Lesic, B.1    Carniel, E.2
  • 38
    • 0034191993 scopus 로고    scopus 로고
    • Horizontal transfer of catalase peroxidase genes between archaea and pathogenic bacteria
    • 10.1016/S0168-9525(00)02007-2, 10782109
    • Faguy D, Doolittle W. Horizontal transfer of catalase peroxidase genes between archaea and pathogenic bacteria. Trends Genet: TIG 2000, 16(5):196. 10.1016/S0168-9525(00)02007-2, 10782109.
    • (2000) Trends Genet: TIG , vol.16 , Issue.5 , pp. 196
    • Faguy, D.1    Doolittle, W.2
  • 39
    • 35349003200 scopus 로고    scopus 로고
    • Bacterial pathogenomics
    • 10.1038/nature06248, 17943120
    • Pallen M, Wren B. Bacterial pathogenomics. Nature 2007, 449(7164):835-842. 10.1038/nature06248, 17943120.
    • (2007) Nature , vol.449 , Issue.7164 , pp. 835-842
    • Pallen, M.1    Wren, B.2
  • 40
    • 35349014651 scopus 로고    scopus 로고
    • Bacterial genome sequencing and its use in infectious diseases
    • 10.1016/S1473-3099(07)70260-8, 17961857
    • Fournier P, Drancourt M, Raoult D. Bacterial genome sequencing and its use in infectious diseases. Lancet Infectious Diseases 2007, 7(11):711-723. 10.1016/S1473-3099(07)70260-8, 17961857.
    • (2007) Lancet Infectious Diseases , vol.7 , Issue.11 , pp. 711-723
    • Fournier, P.1    Drancourt, M.2    Raoult, D.3
  • 41
    • 13444269018 scopus 로고    scopus 로고
    • Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
    • Wan X, Xu D, Kleinhofs A, Zhou J. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evolutionary Biol 2004, 4:19.
    • (2004) BMC Evolutionary Biol , vol.4 , pp. 19
    • Wan, X.1    Xu, D.2    Kleinhofs, A.3    Zhou, J.4
  • 42
    • 0037716514 scopus 로고    scopus 로고
    • Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages
    • 10.1016/S0006-291X(03)00973-2, 12788106
    • Chen L, Zhang C. Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem Biophys Res Commun 2003, 306:310-317. 10.1016/S0006-291X(03)00973-2, 12788106.
    • (2003) Biochem Biophys Res Commun , vol.306 , pp. 310-317
    • Chen, L.1    Zhang, C.2
  • 43
    • 28544451203 scopus 로고    scopus 로고
    • Environments shape the nucleotide composition of genomes
    • Foerstner K, Von Mering C, Hooper S, Bork P. Environments shape the nucleotide composition of genomes. EMBO R 2005, 6(12):1208-1213.
    • (2005) EMBO R , vol.6 , Issue.12 , pp. 1208-1213
    • Foerstner, K.1    Von Mering, C.2    Hooper, S.3    Bork, P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.