Random PCR-based genome sequencing: A non-divide-and-conquer strategy

DNA Research

Volumn 7, Issue 1, 2000, Pages 19-26

  Nishigaki, Koichi ^a   Akasaka, Koichiro ^a   Hasegawa, Takashi ^a  

^a SAITAMA UNIVERSITY   (Japan)

Author keywords

Genome sequencing; PCR relay; Random PCR; Shotgun; Strategy

Indexed keywords

ESCHERICHIA COLI;

BACTERIAL DNA;

ARTICLE; BACTERIAL GENOME; DNA SEQUENCE; ESCHERICHIA COLI; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 0034723449     PISSN: 13402838     EISSN: None     Source Type: Journal    
DOI: 10.1093/dnares/7.1.19     Document Type: Article

References (28)

1. Gauffeau, A. et al. 1997, The yeast, genome directory, Nature, 387 (6547S), 5-105.
2. Tomb, J. F., White, O., Kerlavage, A. R. et al. 1007, The complete genome sequence of the gastric pathogen Helicobacter pylori, Nature, 388, 539-547.
3. Blattner, F. R., Plunkett, G., Bloch, C. A. et al. 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1453-1474.
4. Adams, M. D., Kerlavage, A. R., Fleischmann, R. D. et al. 1995, The genome directory, Nature, 377 (6547S), 3 379.
5. Schuler, G. D., Boguski, M. S., Stewart, E. A. et al. 1995, A gene map of the human genome, Science, 274, 540-546.
6. Venter, J. C., Smith, H. O., and Hood, L. 1990, A new strategy for genome sequencing, Nature, 381, 364-366.
7. Weber, L. J. and Myers, E. M. 1997, Human whole-genome shotgun sequencing, Genome Research, 7, 401-409.
8. Green, P. 1997, Against a whole-genome shotgun, Genome Research, 7, 410-417.
9. Venter, J. C., Adams, M. D., Sutton, G. G., Kerlavage, A. R., Smith, H. O., and Hunkapiller, M. 1998, Shotgun sequencing of the human genome, Science, 280, 1540-1542.
10. Waterston, R. and Sulston J. E. 1998, The human genome project reaching the finishing line, Science, 282, 53-54.
11. Mahairas, G. G., Wallace, J. C., Smith, K. et al. 1999, Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome, Proc. Natl. Acad. Sci. USA, 96, 9739-9744.
12. Roach, J. C., Siegel, A. F., Van den Engh, G., Trask, B., and Hood, L. 1999, Gaps in the human genome project, Nature, 401, 843-845.
13. Davison, A. J. 1991, Experience in shotgun sequencing a 134 kilobase pair DNA molecule, DNA Seq., 1, 389-394.
14. Fleischmann, R. D., Adams, M. D., White, O. et al. 1995, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd., Science, 269, 469-512.
15. Fraser, C. M. and Fleischmann, R. D. 1997, Strategies for whole microbial genome sequencing and analysis, Electrophoresis, 18, 1207-1216.
16. Churcher, C., Bowman, S., Badcock, K. A. et al. 1997, The nucleotide sequence of Saccharomyces cerevisiae chromosome IX, Nature, 387, 84-87.
17. Nishigaki, K., Kinoshita, Y., Sakuma, Y., Nakabayashi, Y., Kyono, H., and Husimi, Y. 1903. Tetramer-library-based strategy for voluminous genome sequencing. Sci. Eng. Rep. Saitama Univ., 27, 43-52.
18. Nishigaki, K., Amano, N., Takasawa, T., Kinoshita, Y., and Husimi, Y. 1990, Seibutu-buturi, 30, S230 (in Japanese).
19. Sakuma, Y. and Nishigaki, K. 1994, Computer prediction of general PCR products based on dynamical solution structures of DNA, J. Biochem., 116, 736-741.
20. Shyamala, V. and Ames, G. F. 1989, Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR, Gene, 84, 1-8.
21. Sambrook, J., Fritsch, E. F., and Maniatis, T. 1989, Molecular cloning: A laboratory manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
22. Nishigaki, K., Amano, N., and Takasawa, T. 1991, DNA profiling. An approach of systemic characterization, classification, and Comparison of Genomic DNAs, Chem. Lett., 1991, 1097-1100.
23. Hamano, K., Takasawa, T., Kurazono, T., Okuyama, Y., and Nishigaki, K. 1996, Genome Profiling: Establishment and practical evaluation of its methodology, Nikkashi, 1996, 54-61.
24. Rosenthal, A. and Jones, D. S. C. 1990, Genomic walking and sequencing by oligo-cassette mediated polymerase chain reaction, Nucleic Acids Res., 18, 3095-3096.
25. Collasius, M., Puchta, H., Schlenker, S., and Valet, G. 1991, Analysis of unknown DNA sequences by polymerase chain reaction (PCR) using a single specific primer and a standardized adaptor, J. Virol Methods, 32, 115-119.
26. Saito, A. and Nishigaki., K. 1999, Estimation of the Redundancy in Human Genome Shotgun Sequencing by a Monte-Carlo Simulation, J. Chem. Software, 5, 29-38.
27. Kinoshita, Y., Nishigaki, K., and Husimi., Y. 1992, Enzymatic synthesis of sequencing primers based on a library of tetramers, Chem. Express, 7, 149-152.
28. Marshall, E. 1998, NIH to produce a 'working draft' of the genome by 2001, Science, 281, 1774-1775.