메뉴 건너뛰기




Volumn 20, Issue 2, 2009, Pages 116-127

Identification of optimal protocols for sequencing difficult templates: Results of the 2008 ABRF DNA sequencing research group difficult template study 2008

Author keywords

Difficult template; DNA sequencing; Research group study

Indexed keywords

DNA; PRIMER DNA;

EID: 68249138823     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (4)

References (30)
  • 2
    • 24044455869 scopus 로고    scopus 로고
    • Genome-sequencing in micro-fabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, et al. Genome-sequencing in micro-fabricated high-density picolitre reactors. Nature 2005;437:376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 3
    • 77953670773 scopus 로고    scopus 로고
    • ABI PRISM® BigDye™ Terminator v3.1 Cycle Sequencing Kit: Protocol: Rev A. Part number 4337035. Applied Biosystems, Foster City, CA, 2002.
    • ABI PRISM® BigDye™ Terminator v3.1 Cycle Sequencing Kit: Protocol: Rev A. Part number 4337035. Applied Biosystems, Foster City, CA, 2002.
  • 4
    • 77953674942 scopus 로고    scopus 로고
    • Automated DNA Sequencing Chemistry Guide. Part number 4305080B. Applied Biosystems, Foster City, CA, 2000.
    • Automated DNA Sequencing Chemistry Guide. Part number 4305080B. Applied Biosystems, Foster City, CA, 2000.
  • 5
    • 0036143303 scopus 로고    scopus 로고
    • Capillary electrophoresis sequencing: Maximum read length at minimal cost
    • Azadan RJ, Fogleman JC, Danielson PB. Capillary electrophoresis sequencing: Maximum read length at minimal cost. Bio-Techniques 2002;32:24-28.
    • (2002) Bio-Techniques , vol.32 , pp. 24-28
    • Azadan, R.J.1    Fogleman, J.C.2    Danielson, P.B.3
  • 6
    • 0028317655 scopus 로고
    • Automated cycle sequencing of PCR templates: Relationships between fragment size, concentration and strand renaturation rates on sequencing efficiency
    • Taylor GO, Dunn IS. Automated cycle sequencing of PCR templates: Relationships between fragment size, concentration and strand renaturation rates on sequencing efficiency. DNA Sequence - The Journal of Sequencing and Mapping 1994;5:9-15.
    • (1994) DNA Sequence - The Journal of Sequencing and Mapping , vol.5 , pp. 9-15
    • Taylor, G.O.1    Dunn, I.S.2
  • 7
    • 0006962619 scopus 로고
    • Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage DNA polymerase and E. coli DNA polymerase I
    • Tabor S, Richardson CC. Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage DNA polymerase and E. coli DNA polymerase I. Proc Natl Acad Sci USA 1989;86:4076-4080.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 4076-4080
    • Tabor, S.1    Richardson, C.C.2
  • 8
    • 0029147334 scopus 로고
    • Accuracy of automated DNA sequencing: A multi-laboratory comparison of sequencing results
    • Naeve CW, Buck GA, Niece RL, Pon RT, Robertson M, Smith AJ. Accuracy of automated DNA sequencing: A multi-laboratory comparison of sequencing results. BioTechniques 1995;19:448-453.
    • (1995) BioTechniques , vol.19 , pp. 448-453
    • Naeve, C.W.1    Buck, G.A.2    Niece, R.L.3    Pon, R.T.4    Robertson, M.5    Smith, A.J.6
  • 9
    • 0025016545 scopus 로고
    • An improved method for sequencing double stranded plasmid DNA from minipreps using DMSO and modified template preparation
    • Seto D. An improved method for sequencing double stranded plasmid DNA from minipreps using DMSO and modified template preparation. Nucleic Acid Res 1990;18:5905.
    • (1990) Nucleic Acid Res , vol.18 , pp. 5905
    • Seto, D.1
  • 10
    • 0030801531 scopus 로고    scopus 로고
    • A DNA cycle sequencing reaction that minimizes compressions on automated fluorescent sequencers
    • Yamakawa H. Ohara O. A DNA cycle sequencing reaction that minimizes compressions on automated fluorescent sequencers. Nucleic Acid Res 1997;25:1311-1312.
    • (1997) Nucleic Acid Res , vol.25 , pp. 1311-1312
    • Yamakawa, H.1    Ohara, O.2
  • 13
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998;8:175-185.
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 14
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing BG, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998;8:186-194.
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.G.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 15
    • 33947395029 scopus 로고    scopus 로고
    • Fundamentals of sequencing of difficult templates - An overview
    • Kieleczawa J. Fundamentals of sequencing of difficult templates - An overview. J Biomol Tech 2006;17:207-217.
    • (2006) J Biomol Tech , vol.17 , pp. 207-217
    • Kieleczawa, J.1
  • 16
    • 33644866775 scopus 로고    scopus 로고
    • Simple modifications of the standard DNA sequencing protocol allow for sequencing through siRNA hairpins and other repeats
    • Kieleczawa J. Simple modifications of the standard DNA sequencing protocol allow for sequencing through siRNA hairpins and other repeats. J Biomol Tech 2005;16:220-223.
    • (2005) J Biomol Tech , vol.16 , pp. 220-223
    • Kieleczawa, J.1
  • 17
    • 0034081243 scopus 로고    scopus 로고
    • Sequencing difficult DNA templates using membrane-mediated loading with hot sample application
    • Gerstner A, Sasvari-Szekely M, Kalasz H, Guttman A. Sequencing difficult DNA templates using membrane-mediated loading with hot sample application. BioTechniques 2000;28:628-630.
    • (2000) BioTechniques , vol.28 , pp. 628-630
    • Gerstner, A.1    Sasvari-Szekely, M.2    Kalasz, H.3    Guttman, A.4
  • 18
    • 0037502226 scopus 로고    scopus 로고
    • Overcoming obstacles in DNA sequencing of expression plasmids for short interfering RNAs
    • Ducat DC, Herrera FJ, Triezenberg SJ. Overcoming obstacles in DNA sequencing of expression plasmids for short interfering RNAs. BioTechniques 2003;34:1140-1144.
    • (2003) BioTechniques , vol.34 , pp. 1140-1144
    • Ducat, D.C.1    Herrera, F.J.2    Triezenberg, S.J.3
  • 19
    • 0242695049 scopus 로고    scopus 로고
    • Blocking oligonucleotides improve sequencing through inverted repeats
    • Esposito D, Gillette W, Hartley JL. Blocking oligonucleotides improve sequencing through inverted repeats. BioTechniques 2003;35:914-920.
    • (2003) BioTechniques , vol.35 , pp. 914-920
    • Esposito, D.1    Gillette, W.2    Hartley, J.L.3
  • 20
    • 0036338149 scopus 로고    scopus 로고
    • Sequencing of difficult templates containing poly (A/T) tracts: Closure of sequencing gaps
    • Langan JE, Rowbottom L, Liloglou T, Field JK, Risk JM. Sequencing of difficult templates containing poly (A/T) tracts: Closure of sequencing gaps. BioTechniques 2002;33:276-280.
    • (2002) BioTechniques , vol.33 , pp. 276-280
    • Langan, J.E.1    Rowbottom, L.2    Liloglou, T.3    Field, J.K.4    Risk, J.M.5
  • 22
    • 0001725994 scopus 로고    scopus 로고
    • Sequencing telomeric DNA templates with short tandem repeats using dye terminator cycle sequencing
    • Zhao X, Haqqi T, Yadav SP. Sequencing telomeric DNA templates with short tandem repeats using dye terminator cycle sequencing. J Biomol Tech 2000;11:111-121.
    • (2000) J Biomol Tech , vol.11 , pp. 111-121
    • Zhao, X.1    Haqqi, T.2    Yadav, S.P.3
  • 23
    • 34547393478 scopus 로고    scopus 로고
    • DNA sequencing of a moderately difficult template: Evaluation of the results from a Thermus thermophilus unknown test sample
    • Adams PS, Dolejsi MK, Hardin S, et al. DNA sequencing of a moderately difficult template: Evaluation of the results from a Thermus thermophilus unknown test sample. BioTechniques 1996;21:678.
    • (1996) BioTechniques , vol.21 , pp. 678
    • Adams, P.S.1    Dolejsi, M.K.2    Hardin, S.3
  • 25
    • 77953654234 scopus 로고    scopus 로고
    • Assessing the quantity and integrity of RNA and DNA following nucleic acid purification
    • Kieleczawa J ed, Sudbury, MA: Jones and Bartlett
    • Willfinger WW, Mackey K, Chomczynski P. Assessing the quantity and integrity of RNA and DNA following nucleic acid purification. In Kieleczawa J (ed): DNA Sequencing: Optimizing Preparation and Cleanup. Sudbury, MA: Jones and Bartlett, 2006;291-312.
    • (2006) DNA Sequencing: Optimizing Preparation and Cleanup , pp. 291-312
    • Willfinger, W.W.1    Mackey, K.2    Chomczynski, P.3
  • 26
    • 0004136246 scopus 로고    scopus 로고
    • 3rd ed. Cold Spring Harbor, NY: CSH Laboratory Press
    • Sambrook J, Russell DW. Molecular Cloning, 3rd ed. Cold Spring Harbor, NY: CSH Laboratory Press, 2001.
    • (2001) Molecular Cloning
    • Sambrook, J.1    Russell, D.W.2
  • 27
    • 77953676884 scopus 로고    scopus 로고
    • Sequencing through various secondary structures: Detailed studies of pDEST vectors and other DNA templates with hairpins
    • Kieleczawa J ed, Sudbury, MA: Jones and Bartlett
    • Li T, Ait-Zahra M, Wu P, Kieleczawa J. Sequencing through various secondary structures: Detailed studies of pDEST vectors and other DNA templates with hairpins. In Kieleczawa J (ed): DNA Sequencing III: Dealing with Difficult Templates. Sudbury, MA: Jones and Bartlett, 2008;109-123.
    • (2008) DNA Sequencing III: Dealing with Difficult Templates , pp. 109-123
    • Li, T.1    Ait-Zahra, M.2    Wu, P.3    Kieleczawa, J.4
  • 28
    • 77953672689 scopus 로고    scopus 로고
    • Improving sequence results from difficult templates with Phi 29 DNA polymerase and nucleotide analogs: The TempliPhi Sequence Resolver Kit
    • Kieleczawa J ed, Sudbury MA: Jones and Bartlett
    • Xiao H, Fuller CW. Improving sequence results from difficult templates with Phi 29 DNA polymerase and nucleotide analogs: The TempliPhi Sequence Resolver Kit. In Kieleczawa J (ed): DNA Sequencing III: Dealing with Difficult Templates. Sudbury MA: Jones and Bartlett, 2008:91-108.
    • (2008) DNA Sequencing III: Dealing with Difficult Templates , pp. 91-108
    • Xiao, H.1    Fuller, C.W.2
  • 29
    • 77953665488 scopus 로고    scopus 로고
    • Solutions for sequencing difficult regions
    • Kieleczawa J ed, Sudbury MA: Jones and Bartlett
    • Yang A. Solutions for sequencing difficult regions. In Kieleczawa J (ed): DNA Sequencing III: Dealing with Difficult Templates. Sudbury MA: Jones and Bartlett, 2008:65-90.
    • (2008) DNA Sequencing III: Dealing with Difficult Templates , pp. 65-90
    • Yang, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.