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Contiguation of Bacterial Clones

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Part of the Methods in Molecular Biology™ book series (MIMB,volume 175)


For accurate assembly of a bacterial clone map (or contig), it is necessary to precisely detect the degree of overlap and map order of clones. One way is to generate fingerprints for all the clones in a given project. The overlap between clones is determined by the proportion of comigrating restriction fragments on either acrylamide or agarose gels, with mulitfold coverage of clones allowing rapid identification of artifacts such as rearranged or deleted clones.


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  1. Coulson, A., Sulston, J. E., Brenner, S., and Jonathon, K. (1986) Towards a physical map of the genome of the nematode Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 83, 7821–7825.

    Article  PubMed  CAS  Google Scholar 

  2. Carrano, A. V., Lamerdin, J., Ashworth, L. K., Watkins, B., Branscomb, E., Slezak, T., et al. (1989) A high-resolution, fluorescence-based, semisutomated method for DNA fingerprinting. Genomics 4, 129–136.

    Article  PubMed  CAS  Google Scholar 

  3. Gregory, S. G., Howell, G. R., and Bentley, D. R. (1997) Genome mapping by fluorescent fingerprinting. Genome Res. 7(12), 1162–1168.

    PubMed  CAS  Google Scholar 

  4. Ding, Y., Johnson, M. D., Colayco, R., Chen, Y. J., Meloyk, J., Schmitt, H., and Shizuya, H. (1999) Contig assembly of bacterial artificial chromosomes clones through multiplexed fluoresence-labeled fingerprinting. Genomics 56, 237–246.

    Article  PubMed  CAS  Google Scholar 

  5. Marra, M. A., Kucaba, T. A., Dietrich, N. L., Green, E. D., Brownstein, B., Wilson, R. K., McDonald, K. M., Hillier, L. W., McPherson, J. D., and Waterson, R. H. (1997) High throughput fingerprinting analysis of large-insert clones. Genome Res. 7(11), 1072–1084.

    PubMed  CAS  Google Scholar 

  6. Osoegawa, K., Yeong Woon, P., Zhao, B., Frengen, E., Tateno, M., Catanese, J. J., and de Jong P. J. (1998) An improved approach for construction of bacterial artificial chromosome libraries. Genomics 52, 1–8.

    Google Scholar 

  7. Ausbel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K. (1995) Current Protocols in Molecular Biology, Greene and Wiley-Interscience, New York.

    Google Scholar 

  8. Southern, E.M. (1975) Detection of specific sequences amongst DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503–517.

    Article  PubMed  CAS  Google Scholar 

  9. Feinberg, A. P. and Vogelstein, B. (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 16–13.

    Article  Google Scholar 

  10. Feinberg, A. P. and Vogelstein, B (1984) Addenum to a technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 137, 266–267.

    Article  PubMed  CAS  Google Scholar 

  11. Birnboim, H. C. and Doly, J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7, 1513–1523.

    Article  PubMed  CAS  Google Scholar 

  12. Gibson, T. J. and Sulston, J. E. (1987) Preparation of Large numbers of plasmid DNA samples in microtiter plates by the alkaline lysis method. Gene Anal. Technol. 24, 41–44.

    Article  Google Scholar 

  13. Ioannou, P. A., Amemiya, C. T., Games, J., Kroised, P. M., Shizuya, H., Chen, C., Batzer, M. A., and de Jong, P. J. (1994) A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genet. 6, 84–89.

    Article  PubMed  CAS  Google Scholar 

  14. Human Genome Mapping Project

  15. South, A. P., Cabal, A., Ives, J. H., James, C. H., Mirza, G., Marenholz, I., Mischke, D., Bacendorf, C., Ragoussis, J., and Nizetic, D. (1999) Human epidermal differentiation complex in a single 2.5Mbp long continuum of overlapping DNA cloned in bacteria integrating physical and transcript maps. J. Invest. Dermatol. 112, 910–918.

    Article  PubMed  CAS  Google Scholar 

  16. Brown, W. R. A. and Bird, A. P. (1986) Long-range restriction site mapping of mammalian genomic DNA. Nature 322, 477–481.

    Article  PubMed  CAS  Google Scholar 

  17. Bird, A. P. (1986) CpG-rich islands and the function of DNA methylation. Nature 321, 209–213.

    Article  PubMed  CAS  Google Scholar 

  18. Sulston, J. E., Mallet, F., Staden, R., Durbin, R., Horsnell, T., and Coulson, A. (1988) Software for genome mapping by fingerprinting techniques CABIOS 4, 125–132.

    PubMed  CAS  Google Scholar 

  19. Soderlund, C., Longden, I., and Mott, R (1997) FPC: a system for building contigs from restriction fingerprinted clones. CABIOS 13, 523–535.

    PubMed  CAS  Google Scholar 

  20. Soderlund, C., Gregory, S. G., and Dunham I. (1998) Sequence ready clone maps, in Guide to Human Genome Computing (Bishop, M. J., ed.), Academic, San Diego, CA, pp. 151–179.

    Chapter  Google Scholar 

  21. Durbin, R. and Thierry-Mieg, J. (1994) The ACEDB genome database, in Computation Methods in Genome Research. (Suhai, S., ed.), Plenum, London, pp. 110–158.

    Google Scholar 

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© 2001 Humana Press Inc., Totowa, NJ

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Humphray, S.J., Knaggs, S.J., Ragoussis, I. (2001). Contiguation of Bacterial Clones. In: Starkey, M.P., Elaswarapu, R. (eds) Genomics Protocols. Methods in Molecular Biology™, vol 175. Humana Press.

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  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-774-8

  • Online ISBN: 978-1-59259-235-7

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