메뉴 건너뛰기




Volumn 155, Issue 1, 2011, Pages 68-77

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

Author keywords

G+C content; High throughput sequencing; Secondary structures; Sequencing bias

Indexed keywords

ACARBOSE; ACTINOPLANES SP; ASSEMBLY ALGORITHM; ASSEMBLY PROCESS; BIOSYNTHESIS GENE CLUSTER; DNA FRAGMENT; G+C CONTENT; GAP REGIONS; GENE CLUSTERS; GENOMIC REGIONS; HIGH-THROUGHPUT; LIFE-SCIENCES; MANUAL INTERVENTION; MANUAL WORK; MICROBIAL GENOMES; PYROSEQUENCING; SECONDARY STRUCTURES; SELF-ANNEALING; SEQUENCING BIAS; STEM-LOOP STRUCTURES; ULTRA-FAST;

EID: 79961209508     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2011.04.010     Document Type: Article
Times cited : (30)

References (41)
  • 2
    • 33646849728 scopus 로고    scopus 로고
    • Rho-dependent transcription termination: more questions than answers
    • Banerjee S., Chalissery J., Bandey I., Sen R. Rho-dependent transcription termination: more questions than answers. J. Microbiol. 2006, 44(1):11-22.
    • (2006) J. Microbiol. , vol.44 , Issue.1 , pp. 11-22
    • Banerjee, S.1    Chalissery, J.2    Bandey, I.3    Sen, R.4
  • 3
    • 42949123953 scopus 로고    scopus 로고
    • Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer
    • Bashir A., Volik S., Collins C., Bafna V., Raphael B.J. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput. Biol. 2008, 4:e1000051.
    • (2008) PLoS Comput. Biol. , vol.4
    • Bashir, A.1    Volik, S.2    Collins, C.3    Bafna, V.4    Raphael, B.J.5
  • 4
    • 65949124252 scopus 로고    scopus 로고
    • Organization of the genes encoding the biosynthesis of actagardine and engineering of a variant generation system
    • Boakes S., Cortés J., Appleyard A.N., Rudd B.A.M., Dawson M.J. Organization of the genes encoding the biosynthesis of actagardine and engineering of a variant generation system. Mol. Microbiol. 2009, 72:1126-1136.
    • (2009) Mol. Microbiol. , vol.72 , pp. 1126-1136
    • Boakes, S.1    Cortés, J.2    Appleyard, A.N.3    Rudd, B.A.M.4    Dawson, M.J.5
  • 5
    • 77955106376 scopus 로고    scopus 로고
    • Organization of the biosynthetic genes encoding deoxyactagardine B (DAB), a new lantibiotic produced by Actinoplanes liguriae NCIMB41362
    • Boakes S., Appleyard A.N., Cortés J., Dawson M.J. Organization of the biosynthetic genes encoding deoxyactagardine B (DAB), a new lantibiotic produced by Actinoplanes liguriae NCIMB41362. J. Antibiot. (Tokyo) 2010, 63(7):351-358.
    • (2010) J. Antibiot. (Tokyo) , vol.63 , Issue.7 , pp. 351-358
    • Boakes, S.1    Appleyard, A.N.2    Cortés, J.3    Dawson, M.J.4
  • 6
    • 0018413311 scopus 로고
    • Inhibition of human intestinal alpha-glucosidehydrolases by a new complex oligosaccharide
    • Caspary W.F., Graf S. Inhibition of human intestinal alpha-glucosidehydrolases by a new complex oligosaccharide. Res. Exp. Med. 1979, 175(1):1-6.
    • (1979) Res. Exp. Med. , vol.175 , Issue.1 , pp. 1-6
    • Caspary, W.F.1    Graf, S.2
  • 8
    • 1942499458 scopus 로고    scopus 로고
    • An assessment of the sequence gaps: unfinished business in a finished human genome
    • Eichler E.E., Clark R.A., She X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nat. Rev. Genet. 2004, 5:345-354.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 345-354
    • Eichler, E.E.1    Clark, R.A.2    She, X.3
  • 9
    • 0036889014 scopus 로고    scopus 로고
    • The value of complete microbial genome sequencing (you get what you pay for)
    • Fraser C.M., Eisen J.A., Nelson K.E., Paulsen I.T., Salzberg S.L. The value of complete microbial genome sequencing (you get what you pay for). J. Bacteriol. 2002, 184(23):6403-6405.
    • (2002) J. Bacteriol. , vol.184 , Issue.23 , pp. 6403-6405
    • Fraser, C.M.1    Eisen, J.A.2    Nelson, K.E.3    Paulsen, I.T.4    Salzberg, S.L.5
  • 10
  • 16
    • 67649379025 scopus 로고    scopus 로고
    • Identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway
    • Kaysser L., Lutsch L., Siebenberg S., Wemakor E., Kammerer B., Gust B. Identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway. J. Biol. Chem. 2009, 284(22):14987-14996.
    • (2009) J. Biol. Chem. , vol.284 , Issue.22 , pp. 14987-14996
    • Kaysser, L.1    Lutsch, L.2    Siebenberg, S.3    Wemakor, E.4    Kammerer, B.5    Gust, B.6
  • 17
    • 34447499141 scopus 로고    scopus 로고
    • Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    • Kingsford C.L., Ayanbule K., Salzberg S.L. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 2007, 8(2):R22.
    • (2007) Genome Biol. , vol.8 , Issue.2
    • Kingsford, C.L.1    Ayanbule, K.2    Salzberg, S.L.3
  • 20
    • 38549144166 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
    • Liolios K., Mavromatis K., Tavernarakis N., Kyrpides N.C. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008, 36:D475-D479.
    • (2008) Nucleic Acids Res. , vol.36
    • Liolios, K.1    Mavromatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 21
    • 0028787036 scopus 로고
    • Template secondary structure can increase the error frequency of the DNA polymerase from Thermus aquaticus
    • Loewen P.C., Switala J. Template secondary structure can increase the error frequency of the DNA polymerase from Thermus aquaticus. Gene 1995, 164:59-63.
    • (1995) Gene , vol.164 , pp. 59-63
    • Loewen, P.C.1    Switala, J.2
  • 22
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis E.R. Next-generation DNA sequencing methods. Annu. Rev. Genom. Human Genet. 2008, 9:387-402.
    • (2008) Annu. Rev. Genom. Human Genet. , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 23
    • 0032528128 scopus 로고    scopus 로고
    • Localised sequence regions possessing high melting temperatures prevent the amplification of a DNA mimic in competitive PCR
    • McDowell D.G., Burns N.A., Parkes H.C. Localised sequence regions possessing high melting temperatures prevent the amplification of a DNA mimic in competitive PCR. Nucleic Acids Res. 1998, 26:3340-3347.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3340-3347
    • McDowell, D.G.1    Burns, N.A.2    Parkes, H.C.3
  • 24
    • 67649976624 scopus 로고    scopus 로고
    • Occurrence, divergence and evolution of intrinsic terminators across eubacteria
    • Mitra A., Angamuthu K., Jayashree H.V., Nagaraja V. Occurrence, divergence and evolution of intrinsic terminators across eubacteria. Genomics 2009, 94(2):110-116.
    • (2009) Genomics , vol.94 , Issue.2 , pp. 110-116
    • Mitra, A.1    Angamuthu, K.2    Jayashree, H.V.3    Nagaraja, V.4
  • 25
    • 70449729788 scopus 로고    scopus 로고
    • Transcription attenuation in bacteria: theme and variations
    • Naville M., Gautheret D. Transcription attenuation in bacteria: theme and variations. Brief. Funct. Genomic. Proteomic. 2009, 8:482-492.
    • (2009) Brief. Funct. Genomic. Proteomic. , vol.8 , pp. 482-492
    • Naville, M.1    Gautheret, D.2
  • 26
    • 61649104320 scopus 로고    scopus 로고
    • The gac-gene cluster for the production of acarbose from Streptomyces glaucescens GLA.O: identification, isolation and characterization
    • Rockser Y., Wehmeier U.F. The gac-gene cluster for the production of acarbose from Streptomyces glaucescens GLA.O: identification, isolation and characterization. J. Biotechnol. 2009, 140:114-123.
    • (2009) J. Biotechnol. , vol.140 , pp. 114-123
    • Rockser, Y.1    Wehmeier, U.F.2
  • 27
    • 34248199933 scopus 로고    scopus 로고
    • Amplification of GC-rich genes by following a combination strategy of primer design, enhancers and modified PCR cycle conditions
    • Sahdev S., Saini S., Tiwari P., Saxena S., Singh Saini K. Amplification of GC-rich genes by following a combination strategy of primer design, enhancers and modified PCR cycle conditions. Mol. Cell. Probes 2007, 21:303-307.
    • (2007) Mol. Cell. Probes , vol.21 , pp. 303-307
    • Sahdev, S.1    Saini, S.2    Tiwari, P.3    Saxena, S.4    Singh Saini, K.5
  • 30
    • 3042614052 scopus 로고    scopus 로고
    • Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of Taq polymerase by the disaccharide trehalose
    • Spiess A., Mueller N., Ivell R. Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of Taq polymerase by the disaccharide trehalose. Clin. Chem. 2004, 50:1256-1259.
    • (2004) Clin. Chem. , vol.50 , pp. 1256-1259
    • Spiess, A.1    Mueller, N.2    Ivell, R.3
  • 33
    • 0029000232 scopus 로고
    • Use of deoxyinosine in PCR to improve amplification of GC-rich DNA
    • Turner S.L., Jenkins F.J. Use of deoxyinosine in PCR to improve amplification of GC-rich DNA. Biotechniques 1995, 19:48-52.
    • (1995) Biotechniques , vol.19 , pp. 48-52
    • Turner, S.L.1    Jenkins, F.J.2
  • 34
    • 0035834664 scopus 로고    scopus 로고
    • Alternate paradigm for intrinsic transcription termination in eubacteria
    • Unniraman S., Prakash R., Nagaraja V. Alternate paradigm for intrinsic transcription termination in eubacteria. J. Biol. Chem. 2001, 276(45):41850-41855.
    • (2001) J. Biol. Chem. , vol.276 , Issue.45 , pp. 41850-41855
    • Unniraman, S.1    Prakash, R.2    Nagaraja, V.3
  • 36
    • 0032860871 scopus 로고    scopus 로고
    • Template secondary structure promotes polymerase jumping during PCR amplification
    • Viswanathan V.K., Krcmarik K., Cianciotto N.P. Template secondary structure promotes polymerase jumping during PCR amplification. Biotechniques 1999, 27:508-511.
    • (1999) Biotechniques , vol.27 , pp. 508-511
    • Viswanathan, V.K.1    Krcmarik, K.2    Cianciotto, N.P.3
  • 38
    • 61849159296 scopus 로고    scopus 로고
    • Low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-III secretion system in Xanthomonas campestris pv. campestris
    • Watt T.F., Vucur M., Baumgarth B., Watt S.A., Niehaus K. Low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-III secretion system in Xanthomonas campestris pv. campestris. J. Biotechnol. 2009, 140:59-67.
    • (2009) J. Biotechnol. , vol.140 , pp. 59-67
    • Watt, T.F.1    Vucur, M.2    Baumgarth, B.3    Watt, S.A.4    Niehaus, K.5
  • 39
    • 1542299147 scopus 로고    scopus 로고
    • Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose
    • Wehmeier U.F., Piepersberg W. Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose. Appl. Microbiol. Biotechnol. 2004, 63:613-625.
    • (2004) Appl. Microbiol. Biotechnol. , vol.63 , pp. 613-625
    • Wehmeier, U.F.1    Piepersberg, W.2
  • 40
    • 0029752741 scopus 로고    scopus 로고
    • Strategy for controlling preferential amplification and avoiding false negatives in PCR typing
    • Weissensteiner T., Lanchbury J.S. Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. Biotechniques 1996, 21:1102-1108.
    • (1996) Biotechniques , vol.21 , pp. 1102-1108
    • Weissensteiner, T.1    Lanchbury, J.S.2
  • 41
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31(13):3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.