메뉴 건너뛰기




Volumn 4, Issue 1, 2012, Pages

Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84871492020     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/1757-4749-4-20     Document Type: Article
Times cited : (7)

References (61)
  • 2
    • 33947373471 scopus 로고    scopus 로고
    • Salmonella: From pathogenesis to therapeutics
    • DOI 10.1128/JB.01730-06
    • Salmonella: from pathogenesis to therapeutics. Boyle EC, Bishop JL, Grassl GA, Finlay BB, J Bacteriol 2007 189 1489 1495 10.1128/JB.01730-06 17189373 (Pubitemid 46446109)
    • (2007) Journal of Bacteriology , vol.189 , Issue.5 , pp. 1489-1495
    • Boyle, E.C.1    Bishop, J.L.2    Grassl, G.A.3    Finlay, B.B.4
  • 3
    • 78650266413 scopus 로고    scopus 로고
    • Chronic and acute infection of the gall bladder by Salmonella Typhi: Understanding the carrier state
    • 10.1038/nrmicro2490 21113180
    • Chronic and acute infection of the gall bladder by Salmonella Typhi: understanding the carrier state. Gonzalez-Escobedo G, Marshall JM, Gunn JS, Nat Rev Microbiol 2011 9 9 14 10.1038/nrmicro2490 21113180
    • (2011) Nat Rev Microbiol , vol.9 , pp. 9-14
    • Gonzalez-Escobedo, G.1    Marshall, J.M.2    Gunn, J.S.3
  • 4
    • 84862765173 scopus 로고    scopus 로고
    • Shedding light on Salmonella carriers
    • 10.1016/j.tim.2012.04.004 22591832
    • Shedding light on Salmonella carriers. Gopinath S, Carden S, Monack D, Trends Microbiol 2012 20 320 327 10.1016/j.tim.2012.04.004 22591832
    • (2012) Trends Microbiol , vol.20 , pp. 320-327
    • Gopinath, S.1    Carden, S.2    Monack, D.3
  • 6
    • 0033968559 scopus 로고    scopus 로고
    • Widal agglutination test - 100 years later: Still plagued by controversy
    • DOI 10.1136/pmj.76.892.80
    • Widal agglutination test-100 years later: still plagued by controversy. Olopoenia LA, King AL, Postgrad Med J 2000 76 80 84 10.1136/pmj.76.892.80 10644383 (Pubitemid 30069442)
    • (2000) Postgraduate Medical Journal , vol.76 , Issue.892 , pp. 80-84
    • Olopoenia, L.A.1    King, A.L.2
  • 8
    • 0034129439 scopus 로고    scopus 로고
    • Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping
    • DOI 10.1016/S0167-7012(00)00148-2, PII S0167701200001482
    • Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping. Nair S, Schreiber E, Thong KL, Pang T, Altwegg M, J Microbiol Methods 2000 41 35 43 10.1016/S0167-7012(00) 00148-2 10856775 (Pubitemid 30345718)
    • (2000) Journal of Microbiological Methods , vol.41 , Issue.1 , pp. 35-43
    • Nair, S.1    Schreiber, E.2    Thong, K.-L.3    Pang, T.4    Altwegg, M.5
  • 10
    • 84866429669 scopus 로고    scopus 로고
    • Whole-genome sequences and comparative genomics of Salmonella enterica serovar Typhi isolates from patients with fatal and nonfatal typhoid fever in Papua New Guinea
    • 10.1128/JB.01051-12 22933755
    • Whole-genome sequences and comparative genomics of Salmonella enterica serovar Typhi isolates from patients with fatal and nonfatal typhoid fever in Papua New Guinea. Baddam R, Thong KL, Avasthi TS, Shaik S, Yap KP, Teh CS, Chai LC, Kumar N, Ahmed N, J Bacteriol 2012 194 5122 5123 10.1128/JB.01051-12 22933755
    • (2012) J Bacteriol , vol.194 , pp. 5122-5123
    • Baddam, R.1    Thong, K.L.2    Avasthi, T.S.3    Shaik, S.4    Yap, K.P.5    Teh, C.S.6    Chai, L.C.7    Kumar, N.8    Ahmed, N.9
  • 11
    • 77953004087 scopus 로고    scopus 로고
    • Pathogen microevolution in high resolution
    • Pathogen microevolution in high resolution. Aziz RK, Nizet V, Sci Transl Med 2010 2 16 16 4
    • (2010) Sci Transl Med , vol.2 , Issue.16 , pp. 16-4
    • Aziz, R.K.1    Nizet, V.2
  • 12
    • 84864003867 scopus 로고    scopus 로고
    • Genetic fine structure of a Salmonella enterica serovar Typhi strain associated with the 2005 outbreak of typhoid fever in Kelantan, Malaysia
    • 10.1128/JB.00581-12 22689247
    • Genetic fine structure of a Salmonella enterica serovar Typhi strain associated with the 2005 outbreak of typhoid fever in Kelantan, Malaysia. Baddam R, Kumar N, Thong KL, Ngoi ST, Teh CS, Yap KP, Chai LC, Avasthi TS, Ahmed N, J Bacteriol 2012 194 3565 3566 10.1128/JB.00581-12 22689247
    • (2012) J Bacteriol , vol.194 , pp. 3565-3566
    • Baddam, R.1    Kumar, N.2    Thong, K.L.3    Ngoi, S.T.4    Teh, C.S.5    Yap, K.P.6    Chai, L.C.7    Avasthi, T.S.8    Ahmed, N.9
  • 13
    • 33750441484 scopus 로고    scopus 로고
    • M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
    • DOI 10.1186/1471-2105-7-433
    • M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. Treangen T, Messeguer X, BMC Bioinformatics 2006 7 433 10.1186/1471-2105-7-433 17022809 (Pubitemid 44649685)
    • (2006) BMC Bioinformatics , vol.7 , pp. 433
    • Treangen, T.J.1    Messeguer, X.2
  • 14
    • 0036224264 scopus 로고    scopus 로고
    • Salmonella enterica serotype Typhimurium ShdA is an outer membrane fibronectin-binding protein that is expressed in the intestine
    • DOI 10.1046/j.1365-2958.2002.02805.x
    • Salmonella enterica serotype Typhimurium ShdA is an outer membrane fibronectin-binding protein that is expressed in the intestine. Kingsley RA, Santos RL, Keestra AM, Adams LG, Bäumler AJ, Mol Microbiol 2002 43 895 905 10.1046/j.1365-2958.2002.02805.x 11929540 (Pubitemid 34415714)
    • (2002) Molecular Microbiology , vol.43 , Issue.4 , pp. 895-905
    • Kingsley, R.A.1    Santos, R.L.2    Keestra, A.M.3    Adams, L.G.4    Baumler, A.J.5
  • 15
    • 0034114755 scopus 로고    scopus 로고
    • The shdA gene is restricted to serotypes of Salmonella enterica subspecies I and contributes to efficient and prolonged fecal shedding
    • DOI 10.1128/IAI.68.5.2720-2727.2000
    • The shdA gene is restricted to serotypes of Salmonella enterica subspecies I and contributes to efficient and prolonged fecal shedding. Kingsley RA, van Amsterdam K, Kramer N, Bäumler AJ, Infect Immun 2000 68 2720 2727 10.1128/IAI.68.5.2720-2727.2000 10768965 (Pubitemid 30253847)
    • (2000) Infection and Immunity , vol.68 , Issue.5 , pp. 2720-2727
    • Kingsley, R.A.1    Van Amsterdam, K.2    Kramer, N.3    Baumler, A.J.4
  • 17
    • 2442589577 scopus 로고    scopus 로고
    • Type IV pilus structure and bacterial pathogenicity
    • DOI 10.1038/nrmicro885
    • Type IV pilus structure and bacterial pathogenicity. Craig L, Pique ME, Tainer JA, Nat Rev Microbiol 2004 2 363 378 10.1038/nrmicro885 15100690 (Pubitemid 39490116)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.5 , pp. 363-378
    • Craig, L.1    Pique, M.E.2    Tainer, J.A.3
  • 19
    • 27844499689 scopus 로고    scopus 로고
    • The distinct binding specificities exhibited by enterobacterial type 1 fimbriae are determined by their fimbrial shafts
    • DOI 10.1074/jbc.M501249200
    • The distinct binding specificities exhibited by enterobacterial Type 1 fimbriae are determined by their fimbrial shafts. Duncan MJ, Mann EL, Cohen MS, Ofek I, Sharon N, Abraham SN, J Biol Chem 2005 280 37707 37716 10.1074/jbc.M501249200 16118220 (Pubitemid 41642379)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.45 , pp. 37707-37716
    • Duncan, M.J.1    Mann, E.L.2    Cohen, M.S.3    Ofek, I.4    Sharon, N.5    Abraham, S.N.6
  • 20
    • 66849101496 scopus 로고    scopus 로고
    • FimH alleles direct preferential binding of Salmonella to distinct mammalian cells or to avian cells
    • 10.1099/mic.0.026286-0 19383701
    • FimH alleles direct preferential binding of Salmonella to distinct mammalian cells or to avian cells. Guo A, Cao S, Tu L, Chen P, Zhang C, Jia A, Yang W, Liu Z, Chen H, Schifferli DM, Microbiology 2009 155 1623 1633 10.1099/mic.0.026286-0 19383701
    • (2009) Microbiology , vol.155 , pp. 1623-1633
    • Guo, A.1    Cao, S.2    Tu, L.3    Chen, P.4    Zhang, C.5    Jia, A.6    Yang, W.7    Liu, Z.8    Chen, H.9    Schifferli, D.M.10
  • 21
    • 0029566032 scopus 로고
    • Role of the viaB locus in synthesis, transport and expression of Salmonella typhi Vi antigen
    • Role of the viaB locus in synthesis, transport and expression of Salmonella typhi Vi antigen. Virlogeux I, Waxin H, Ecobichon C, Popoff MY, Microbiology 1995 141 3039 3047 10.1099/13500872-141-12-3039 8574397 (Pubitemid 26011342)
    • (1995) Microbiology , vol.141 , Issue.12 , pp. 3039-3047
    • Virlogeux, I.1    Waxin, H.2    Ecobichon, C.3    Popoff, M.Y.4
  • 22
    • 0021233257 scopus 로고
    • Reexamination of the protective role of the capsular polysaccharide (Vi antigen) of Salmonella typhi
    • Re examination of the protective role of the capsular polysaccharide (Vi antigen) of Salmonella typhi. Robbins JD, Robbins JB, J Infect Dis 1984 150 436 449 10.1093/infdis/150.3.436 6207249 (Pubitemid 14037031)
    • (1984) Journal of Infectious Diseases , vol.150 , Issue.3 , pp. 436-449
    • Robbins, J.D.1    Robbins, J.B.2
  • 24
    • 0030984298 scopus 로고    scopus 로고
    • Regulation of lipid A modifications by Salmonella typhimurium virulence genes phoP-phoQ
    • DOI 10.1126/science.276.5310.250
    • Regulation of lipid A modifications by Salmonella typhimurium virulence genes phoP-phoQ. Guo L, Lim KB, Gunn JS, Bainbridge B, Darveau RP, Hackett M, Miller SI, Science 1997 276 250 253 10.1126/science.276.5310.250 9092473 (Pubitemid 27172682)
    • (1997) Science , vol.276 , Issue.5310 , pp. 250-253
    • Guo, L.1    Lim, K.B.2    Gunn, J.S.3    Bainbridge, B.4    Darveau, R.P.5    Hackett, M.6    Miller, S.I.7
  • 26
    • 14644438364 scopus 로고    scopus 로고
    • Circular genome visualization and exploration using CGView
    • DOI 10.1093/bioinformatics/bti054
    • Circular genome visualization and exploration using CGView. Stothard P, Wishart DS, Bioinformatics 2005 21 537 539 10.1093/bioinformatics/bti054 15479716 (Pubitemid 40310241)
    • (2005) Bioinformatics , vol.21 , Issue.4 , pp. 537-539
    • Stothard, P.1    Wishart, D.S.2
  • 27
    • 0033901978 scopus 로고    scopus 로고
    • Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar typhimurium survival in Peyer's patches
    • DOI 10.1128/JB.182.16.4406-4413.2000
    • Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar typhimurium survival in Peyer's patches. Stanley TL, Ellermeier CD, Slauch JM, J Bacteriol 2000 182 4406 4413 10.1128/JB.182.16.4406-4413.2000 10913072 (Pubitemid 30599802)
    • (2000) Journal of Bacteriology , vol.182 , Issue.16 , pp. 4406-4413
    • Stanley, T.L.1    Ellermeier, C.D.2    Slauch, J.M.3
  • 29
    • 0032478074 scopus 로고    scopus 로고
    • A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage
    • DOI 10.1073/pnas.95.5.2574
    • A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by acryptic bacteriophage. Hardt WD, Urlaub H, Galan JE, Proc Natl Acad Sci U S A 1998 95 2574 2579 10.1073/pnas.95.5.2574 9482928 (Pubitemid 28145984)
    • (1998) Proceedings of the National Academy of Sciences of the United States of America , vol.95 , Issue.5 , pp. 2574-2579
    • Hardt, W.-D.1    Urlaub, H.2    Galan, J.E.3
  • 30
    • 0034060727 scopus 로고    scopus 로고
    • Salmonella pathogenicity islands: Big virulence in small packages
    • DOI 10.1016/S1286-4579(00)00273-2
    • Salmonella pathogenicity islands: big virulence in small packages. Marcus SL, Brumell JH, Pfeifer CG, Finlay BB, Microbes Infect 2000 2 145 156 10.1016/S1286-4579(00)00273-2 10742687 (Pubitemid 30154704)
    • (2000) Microbes and Infection , vol.2 , Issue.2 , pp. 145-156
    • Marcus, S.L.1    Brumell, J.H.2    Pfeifer, C.G.3    Finlay, B.B.4
  • 31
    • 0033066941 scopus 로고    scopus 로고
    • Type III secretion machines and the pathogenesis of enteric infections caused by Yersinia and Salmonella spp.
    • DOI 10.1111/j.1600-065X.1999.tb01296.x
    • Type III secretion machines and the pathogenesis of enteric infections caused by Yersinia and Salmonella spp. Lee VT, Schneewind O, Immunol Rev 1999 168 241 255 10.1111/j.1600-065X.1999.tb01296.x 10399078 (Pubitemid 29276686)
    • (1999) Immunological Reviews , vol.168 , pp. 241-255
    • Lee, V.T.1    Schneewind, O.2
  • 32
    • 59849112843 scopus 로고    scopus 로고
    • Salmonella takes control: Effector driven manipulation of the host
    • 10.1016/j.mib.2008.12.001 19157959
    • Salmonella takes control: effector driven manipulation of the host. McGhie EJ, Brawn LC, Hume PJ, Humphreys D, Koronakis V, Curr Opin Microbiol 2009 12 117 124 10.1016/j.mib.2008.12.001 19157959
    • (2009) Curr Opin Microbiol , vol.12 , pp. 117-124
    • McGhie, E.J.1    Brawn, L.C.2    Hume, P.J.3    Humphreys, D.4    Koronakis, V.5
  • 33
    • 0042195926 scopus 로고    scopus 로고
    • Functions and effectors of the Salmonella pathogenicity island 2 type III secretion system
    • DOI 10.1046/j.1462-5822.2003.00294.x
    • Functions and effectors of the Salmonella pathogenicity island 2 type III secretion system. Waterman SR, Holden DW, Cell Microbiol 2003 5 501 511 10.1046/j.1462-5822.2003.00294.x 12864810 (Pubitemid 36939590)
    • (2003) Cellular Microbiology , vol.5 , Issue.8 , pp. 501-511
    • Waterman, S.R.1    Holden, D.W.2
  • 34
    • 0141480261 scopus 로고    scopus 로고
    • The roles of SsrA-SsrB and OmpR-EnvZ in the regulation of genes encoding the Salmonella typhimurium SPI-2 type III secretion system
    • The roles of SsrA-SsrB and OmpR-EnvZ in the regulation of genes encoding the Salmonella typhimurium SPI-2 type III secretion system. Garmendia J, Beuzón CR, Ruiz-Albert J, Holden DW, Microbiology 2003 149 2385 2396 10.1099/mic.0.26397-0 12949164 (Pubitemid 37160714)
    • (2003) Microbiology , vol.149 , Issue.9 , pp. 2385-2396
    • Garmendia, J.1    Beuzon, C.R.2    Ruiz-Albert, J.3    Holden, D.W.4
  • 36
    • 54049111835 scopus 로고    scopus 로고
    • Cooperation of Salmonella pathogenicity islands 1 and 4 is required to breach epithelial barriers
    • 10.1111/j.1462-5822.2008.01218.x 18671822
    • Cooperation of Salmonella pathogenicity islands 1 and 4 is required to breach epithelial barriers. Gerlach RG, Claudio N, Rohde M, Jackel D, Wagner C, Hensel M, Cell Microbiol 2008 10 2364 2376 10.1111/j.1462-5822.2008.01218.x 18671822
    • (2008) Cell Microbiol , vol.10 , pp. 2364-2376
    • Gerlach, R.G.1    Claudio, N.2    Rohde, M.3    Jackel, D.4    Wagner, C.5    Hensel, M.6
  • 37
    • 0031928971 scopus 로고    scopus 로고
    • Identification of a pathogenicity island required for Salmonella enteropathogenicity
    • DOI 10.1046/j.1365-2958.1998.00984.x
    • Identification of a pathogenicity island required for Salmonella enteropathogenicity. Wood MW, Jones MA, Watson PR, Hedges S, Wallis TS, Galyov EE, Mol Microbiol 1998 29 883 891 10.1046/j.1365-2958.1998.00984.x 9723926 (Pubitemid 28365473)
    • (1998) Molecular Microbiology , vol.29 , Issue.3 , pp. 883-891
    • Wood, M.W.1    Jones, M.A.2    Watson, P.R.3    Hedges, S.4    Wallis, T.S.5    Galyov, E.E.6
  • 40
    • 79959354608 scopus 로고    scopus 로고
    • Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient
    • 10.1128/JB.05006-11 21515762
    • Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient. Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Mégraud F, Ahmed N, J Bacteriol 2011 193 3385 3386 10.1128/JB.05006-11 21515762
    • (2011) J Bacteriol , vol.193 , pp. 3385-3386
    • Avasthi, T.S.1    Devi, S.H.2    Taylor, T.D.3    Kumar, N.4    Baddam, R.5    Kondo, S.6    Suzuki, Y.7    Lamouliatte, H.8    Mégraud, F.9    Ahmed, N.10
  • 41
    • 79961163061 scopus 로고    scopus 로고
    • Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India
    • 10.1128/JB.05413-11 21685291
    • Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. Avasthi TS, Kumar N, Baddam R, Hussain A, Nandanwar N, Jadhav S, Ahmed N, J Bacteriol 2011 193 4272 4273 10.1128/JB.05413-11 21685291
    • (2011) J Bacteriol , vol.193 , pp. 4272-4273
    • Avasthi, T.S.1    Kumar, N.2    Baddam, R.3    Hussain, A.4    Nandanwar, N.5    Jadhav, S.6    Ahmed, N.7
  • 43
    • 80053609595 scopus 로고    scopus 로고
    • Genome of a novel isolate of Paracoccus denitrificans capable of degrading N, N-dimethylformamide
    • 10.1128/JB.05667-11 21914898
    • Genome of a novel isolate of Paracoccus denitrificans capable of degrading N, N-dimethylformamide. Siddavattam D, Karegoudar TB, Mudde SK, Kumar N, Baddam R, Avasthi TS, Ahmed N, J Bacteriol 2011 193 5598 5599 10.1128/JB.05667-11 21914898
    • (2011) J Bacteriol , vol.193 , pp. 5598-5599
    • Siddavattam, D.1    Karegoudar, T.B.2    Mudde, S.K.3    Kumar, N.4    Baddam, R.5    Avasthi, T.S.6    Ahmed, N.7
  • 44
    • 84866375906 scopus 로고    scopus 로고
    • Insights from the genome sequence of a Salmonella enterica serovar Typhi strain associated with a sporadic case of typhoid fever in Malaysia
    • 10.1128/JB.01062-12 22933756
    • Insights from the genome sequence of a Salmonella enterica serovar Typhi strain associated with a sporadic case of typhoid fever in Malaysia. Yap KP, Teh CS, Baddam R, Chai LC, Kumar N, Avasthi TS, Ahmed N, Thong KL, J Bacteriol 2012 194 5124 5125 10.1128/JB.01062-12 22933756
    • (2012) J Bacteriol , vol.194 , pp. 5124-5125
    • Yap, K.P.1    Teh, C.S.2    Baddam, R.3    Chai, L.C.4    Kumar, N.5    Avasthi, T.S.6    Ahmed, N.7    Thong, K.L.8
  • 45
    • 84868620620 scopus 로고    scopus 로고
    • Genome sequence and comparative pathogenomics analysis of a Salmonella enterica serovar Typhi strain associated with a typhoid carrier in Malaysia
    • 10.1128/JB.01416-12 23045488
    • Genome sequence and comparative pathogenomics analysis of a Salmonella enterica serovar Typhi strain associated with a typhoid carrier in Malaysia. Yap KP, Gan HM, Teh CS, Baddam R, Chai LC, Kumar N, Tiruvayipati SA, Ahmed N, Thong KL, J Bacteriol 2012 194 5970 5971 10.1128/JB.01416-12 23045488
    • (2012) J Bacteriol , vol.194 , pp. 5970-5971
    • Yap, K.P.1    Gan, H.M.2    Teh, C.S.3    Baddam, R.4    Chai, L.C.5    Kumar, N.6    Tiruvayipati, S.A.7    Ahmed, N.8    Thong, K.L.9
  • 46
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • DOI 10.1101/gr.074492.107
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 821 829 10.1101/gr.074492.107 18349386 (Pubitemid 351645072)
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 47
    • 79951530130 scopus 로고    scopus 로고
    • Scaffolding pre-assembled contigs using SSPACE
    • 10.1093/bioinformatics/btq683 21149342
    • Scaffolding pre-assembled contigs using SSPACE. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W, Bioinformatics 2011 27 578 579 10.1093/bioinformatics/btq683 21149342
    • (2011) Bioinformatics , vol.27 , pp. 578-579
    • Boetzer, M.1    Henkel, C.V.2    Jansen, H.J.3    Butler, D.4    Pirovano, W.5
  • 48
    • 84871481892 scopus 로고    scopus 로고
    • GapFiller: A de novo assembly approach to fill the gap within paired reads
    • 10.1186/1471-2105-13-S14-S8 22239737
    • GapFiller: a de novo assembly approach to fill the gap within paired reads. Nadalin F, Vezzi F, Policriti A, BMC Bioinformatics 2012 13 14 8 10.1186/1471-2105-13-S14-S8 22239737
    • (2012) BMC Bioinformatics , vol.13 , Issue.14 , pp. 8
    • Nadalin, F.1    Vezzi, F.2    Policriti, A.3
  • 49
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler Transform
    • 10.1093/bioinformatics/btp324 19451168
    • Fast and accurate short read alignment with Burrows-Wheeler Transform. Li H, Durbin R, Bioinformatics 2009 25 1754 1760 10.1093/bioinformatics/btp324 19451168
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 50
    • 77949512406 scopus 로고    scopus 로고
    • Tablet-next generation sequence assembly visualization
    • 10.1093/bioinformatics/btp666 19965881
    • Tablet-next generation sequence assembly visualization. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D, Bioinformatics 2010 26 401 402 10.1093/bioinformatics/btp666 19965881
    • (2010) Bioinformatics , vol.26 , pp. 401-402
    • Milne, I.1    Bayer, M.2    Cardle, L.3    Shaw, P.4    Stephen, G.5    Wright, F.6    Marshall, D.7
  • 51
    • 84868089043 scopus 로고    scopus 로고
    • SEED Servers: High-performance access to the SEED genomes, annotations, and metabolic models
    • 10.1371/journal.pone.0048053
    • SEED Servers: high-performance access to the SEED genomes, annotations, and metabolic models. Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, et al. PLoS ONE 2012 7 10 48053 10.1371/journal.pone.0048053
    • (2012) PLoS ONE , vol.7 , Issue.10 , pp. 48053
    • Aziz, R.K.1    Devoid, S.2    Disz, T.3    Edwards, R.A.4    Henry, C.S.5
  • 52
    • 77951945303 scopus 로고    scopus 로고
    • An Ergatis-based prokaryotic genome annotation web server
    • 10.1093/bioinformatics/btq090 20194626
    • An Ergatis-based prokaryotic genome annotation web server. Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q, Bioinformatics 2010 26 1122 1124 10.1093/bioinformatics/btq090 20194626
    • (2010) Bioinformatics , vol.26 , pp. 1122-1124
    • Hemmerich, C.1    Buechlein, A.2    Podicheti, R.3    Revanna, K.V.4    Dong, Q.5
  • 54
    • 0033485517 scopus 로고    scopus 로고
    • Improved microbial gene identification with GLIMMER
    • 10.1093/nar/27.23.4636 10556321
    • Improved microbial gene identification with GLIMMER. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL, Nucleic Acids Res 1999 27 4636 4641 10.1093/nar/27.23.4636 10556321
    • (1999) Nucleic Acids Res , vol.27 , pp. 4636-4641
    • Delcher, A.L.1    Harmon, D.2    Kasif, S.3    White, O.4    Salzberg, S.L.5
  • 55
    • 0642307369 scopus 로고    scopus 로고
    • EasyGene - A prokaryotic gene finder that ranks ORFs by statistical significance
    • DOI 10.1186/1471-2105-4-21
    • EasyGene-a prokaryotic gene finder that ranks ORFs by statistical significance. Larsen TS, Krogh A, BMC Bioinformatics 2003 4 21 10.1186/1471-2105-4-21 12783628 (Pubitemid 38751249)
    • (2003) BMC Bioinformatics , vol.4 , pp. 21
    • Larsen, T.S.1    Krogh, A.2
  • 57
    • 23144460836 scopus 로고    scopus 로고
    • The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    • DOI 10.1093/nar/gki366
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Schattner P, Brooks AN, Lowe TM, Nucleic Acids Res 2005 33 686 W689 10.1093/nar/gki366 15980563 (Pubitemid 44530010)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Schattner, P.1    Brooks, A.N.2    Lowe, T.M.3
  • 58
    • 84868099390 scopus 로고    scopus 로고
    • PhiSpy: A novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
    • 10.1093/nar/gks406 22584627
    • PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Akhter S, Aziz RK, Edwards RA, Nucleic Acids Res 2012 40 126 10.1093/nar/gks406 22584627
    • (2012) Nucleic Acids Res , vol.40 , pp. 5126
    • Akhter, S.1    Aziz, R.K.2    Edwards, R.A.3
  • 59
    • 33749431828 scopus 로고    scopus 로고
    • Prophage Finder: A prophage loci prediction tool for prokaryotic genome sequences
    • Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. Bose M, Barber RD, In Silico Biol 2006 6 223 227 16922685 (Pubitemid 44508931)
    • (2006) In Silico Biology , vol.6 , Issue.3 , pp. 223-227
    • Bose, M.1    Barber, R.D.2
  • 60
    • 33748689309 scopus 로고    scopus 로고
    • Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands
    • DOI 10.1093/bioinformatics/btl369
    • Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Vernikos GS, Parkhill J, Bioinformatics 2006 22 2196 2203 10.1093/bioinformatics/btl369 16837528 (Pubitemid 44390872)
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2196-2203
    • Vernikos, G.S.1    Parkhill, J.2
  • 61
    • 61449201423 scopus 로고    scopus 로고
    • IslandViewer: An integrated interface for computational identification and visualization of genomic islands
    • 10.1093/bioinformatics/btp030 19151094
    • IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Langille MG, Brinkman FS, Bioinformatics 2009 25 664 665 10.1093/bioinformatics/btp030 19151094
    • (2009) Bioinformatics , vol.25 , pp. 664-665
    • Langille, M.G.1    Brinkman, F.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.