메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Gene fragmentation in bacterial draft genomes: Extent, consequences and mitigation

Author keywords

[No Author keywords available]

Indexed keywords

NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE SYNTHASE; PROTEIN SERINE THREONINE KINASE;

EID: 84855495004     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-14     Document Type: Article
Times cited : (55)

References (31)
  • 2
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • 10.1073/pnas.74.12.5463, 431765, 271968
    • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977, 74:5463-5467. 10.1073/pnas.74.12.5463, 431765, 271968.
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 3
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • 10.1038/nature09796, 21307932
    • Mardis ER. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203. 10.1038/nature09796, 21307932.
    • (2011) Nature , vol.470 , pp. 198-203
    • Mardis, E.R.1
  • 4
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • 10.1016/j.tig.2007.12.007, 18262675
    • Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24:133-141. 10.1016/j.tig.2007.12.007, 18262675.
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 5
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genom Hum G 2008, 9:387-402.
    • (2008) Annu Rev Genom Hum G , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 6
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • 10.1038/nrg2626, 19997069
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 7
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • 10.1016/j.ygeno.2010.03.001, 2874646, 20211242
    • Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95:315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 9
    • 77956543003 scopus 로고    scopus 로고
    • Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim
    • 10.1093/bioinformatics/btq365, 2935434, 20823302
    • Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I. Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim. Bioinformatics 2010, 26:i420-i425. 10.1093/bioinformatics/btq365, 2935434, 20823302.
    • (2010) Bioinformatics , vol.26
    • Balzer, S.1    Malde, K.2    Lanzén, A.3    Sharma, A.4    Jonassen, I.5
  • 10
    • 4544263565 scopus 로고    scopus 로고
    • Fragment assembly with short reads
    • 10.1093/bioinformatics/bth205, 15059830
    • Chaisson M, Pevzner P, Tang H. Fragment assembly with short reads. Bioinformatics 2004, 20:2067-2074. 10.1093/bioinformatics/bth205, 15059830.
    • (2004) Bioinformatics , vol.20 , pp. 2067-2074
    • Chaisson, M.1    Pevzner, P.2    Tang, H.3
  • 12
    • 59949093527 scopus 로고    scopus 로고
    • De novo fragment assembly with short mate-paired reads: does the read length matter?
    • 2652199, 19056694
    • Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: does the read length matter?. Genome Res 2009, 19:336-346. 2652199, 19056694.
    • (2009) Genome Res , vol.19 , pp. 336-346
    • Chaisson, M.J.1    Brinza, D.2    Pevzner, P.A.3
  • 14
    • 74049094093 scopus 로고    scopus 로고
    • The effect of sequencing errors on metagenomic gene prediction
    • 10.1186/1471-2164-10-520, 2781827, 19909532
    • Hoff KJ. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics 2009, 10:520. 10.1186/1471-2164-10-520, 2781827, 19909532.
    • (2009) BMC Genomics , vol.10 , pp. 520
    • Hoff, K.J.1
  • 15
    • 34547588704 scopus 로고    scopus 로고
    • KAAS: an automatic genome annotation and pathway reconstruction server
    • 10.1093/nar/gkm321, 1933193, 17526522
    • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-W185. 10.1093/nar/gkm321, 1933193, 17526522.
    • (2007) Nucleic Acids Res , vol.35
    • Moriya, Y.1    Itoh, M.2    Okuda, S.3    Yoshizawa, A.C.4    Kanehisa, M.5
  • 16
    • 79960394911 scopus 로고    scopus 로고
    • Draft genome sequence of the marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea
    • 10.1128/JB.05097-11, 3133317, 21571991
    • Fan L, Liu Y, Li Z, Baumann HI, Kleinschmidt K, Ye W, Imhoff JF, Kleine M, Cai D. Draft genome sequence of the marine Streptomyces sp. strain PP-C42, isolated from the Baltic Sea. J Bacteriol 2011, 193:3691-3692. 10.1128/JB.05097-11, 3133317, 21571991.
    • (2011) J Bacteriol , vol.193 , pp. 3691-3692
    • Fan, L.1    Liu, Y.2    Li, Z.3    Baumann, H.I.4    Kleinschmidt, K.5    Ye, W.6    Imhoff, J.F.7    Kleine, M.8    Cai, D.9
  • 17
    • 33748631825 scopus 로고    scopus 로고
    • Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms
    • 10.1021/cr0503097, 16895337
    • Fischbach MA, Walsh CT. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 2006, 106:3468-3496. 10.1021/cr0503097, 16895337.
    • (2006) Chem Rev , vol.106 , pp. 3468-3496
    • Fischbach, M.A.1    Walsh, C.T.2
  • 18
    • 77949917076 scopus 로고    scopus 로고
    • Evolution and phyletic distribution of two-component signal transduction systems
    • 10.1016/j.mib.2009.12.011, 20133179
    • Wuichet K, Cantwell BJ, Zhulin IB. Evolution and phyletic distribution of two-component signal transduction systems. Curr Opin Microbiol 2010, 13:219-225. 10.1016/j.mib.2009.12.011, 20133179.
    • (2010) Curr Opin Microbiol , vol.13 , pp. 219-225
    • Wuichet, K.1    Cantwell, B.J.2    Zhulin, I.B.3
  • 20
    • 24944587193 scopus 로고    scopus 로고
    • Towards a genome-based taxonomy for prokaryotes
    • 10.1128/JB.187.18.6258-6264.2005, 1236649, 16159757
    • Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005, 187:6258-6264. 10.1128/JB.187.18.6258-6264.2005, 1236649, 16159757.
    • (2005) J Bacteriol , vol.187 , pp. 6258-6264
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 23
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: prokayotic gene recognition and translation initiation site identification
    • 10.1186/1471-2105-11-119, 2848648, 20211023
    • Hyatt D, Chen G-L, LoCascio PL, Land ML, Larimer FW, Hauser LJ. Prodigal: prokayotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119. 10.1186/1471-2105-11-119, 2848648, 20211023.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.-L.2    LoCascio, P.L.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 24
    • 0000122573 scopus 로고
    • PHYLIP: phylogeny inference package (version 3.2)
    • Felsenstein J. PHYLIP: phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 25
    • 0038561132 scopus 로고    scopus 로고
    • Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis
    • 10.1038/nbt820, 12692562
    • Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 2003, 21:526-531. 10.1038/nbt820, 12692562.
    • (2003) Nat Biotechnol , vol.21 , pp. 526-531
    • Ikeda, H.1    Ishikawa, J.2    Hanamoto, A.3    Shinose, M.4    Kikuchi, H.5    Shiba, T.6    Sakaki, Y.7    Hattori, M.8    Omura, S.9
  • 30
    • 44349169524 scopus 로고    scopus 로고
    • Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350
    • 10.1128/JB.00204-08, 2395044, 18375553
    • Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol 2008, 190:4050-4060. 10.1128/JB.00204-08, 2395044, 18375553.
    • (2008) J Bacteriol , vol.190 , pp. 4050-4060
    • Ohnishi, Y.1    Ishikawa, J.2    Hara, H.3    Suzuki, H.4    Ikenoya, M.5    Ikeda, H.6    Yamashita, A.7    Hattori, M.8    Horinouchi, S.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.