1887
Preview this article:

There is no abstract available.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-145-10-2625
1999-10-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/micro/145/10/1452625a.html?itemId=/content/journal/micro/10.1099/00221287-145-10-2625&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.[CrossRef] [Google Scholar]
  2. Andersson, S. G. E., Zomorodipour, A., Anderssen, J. O. & 7 other authors (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 133–140.[CrossRef] [Google Scholar]
  3. Arigoni, F., Talabot, F., Peitsch, M. & 7 other authors (1998). A genome-based approach for the identification of essential bacterial genes. Nat Biotechnol 16, 851–856.[CrossRef] [Google Scholar]
  4. Azevedo, V., Alvarez, E., Zumstein, E., Damiani, G., Sgaramella, V., Ehrlich, S. D. & Serror, P. (1993). An ordered collection of Bacillus subtilis DNA segments cloned in yeast artificial chromosomes. Proc Natl Acad Sci USA 90, 6047-6051.[CrossRef] [Google Scholar]
  5. Barnes, W. M. (1994). PCR amplification of up to 35 kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc Natl Acad Sci USA 91, 2216-2220.[CrossRef] [Google Scholar]
  6. Beck, E. & Bremer, E. (1980). Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12. Nucleic Acids Res 8, 3011-3027.[CrossRef] [Google Scholar]
  7. Beucher, M. & Sparling, P. F. (1995). Cloning, sequencing, and characterization of the gene encoding FrpB, a major iron-regulated, outer membrane protein of Neisseria gonorrhoeae. J Bacteriol 177, 2041-2049. [Google Scholar]
  8. Blattner, F. R., Plunkett, G., III, Bloch, C. A. & 14 other authors (1997). The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.[CrossRef] [Google Scholar]
  9. Bodenteich, A., Chissoe, S., Wang, Y. F. & Roe, B. A. (1994). Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. In Automated DNA Sequencing and Analysis Techniques. Edited by M. Adams, C. Fields and J. C. Venter. San Diego, CA: Academic Press.
  10. Bolotin, A., Sorokin, A. & Ehrlich, S. D. (1996). Mapping of the 150 kb spoIIIC–pheA region of the Bacillus subtilis chromosome using long accurate PCR and three yeast artificial chromosomes. Microbiology 142, 3017-3020.[CrossRef] [Google Scholar]
  11. Bonfield, J. K., Smith, K. & Staden, R. (1995). A new DNA sequence assembly program. Nucleic Acids Res 23, 4992-4999.[CrossRef] [Google Scholar]
  12. Brosch, R., Gordon, S. V., Billault, A., Garnier, T., Eiglmeier, K., Soravito, C., Barrell, B. G. & Cole, S. T. (1998). Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics. Infect Immun 66, 2221-2229. [Google Scholar]
  13. Cai, W., Jing, J., Irvin, B. & 8 other authors (1998). High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc Natl Acad Sci USA 95, 3390–3395.[CrossRef] [Google Scholar]
  14. Cohen, S. N., Chang, A. C., Boyer, H. W. & Helling, R. B. (1973). Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA 70, 3240-3244.[CrossRef] [Google Scholar]
  15. Cole, S. T., Brosch R., Parkill J. & 39 other authors (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544.[CrossRef] [Google Scholar]
  16. Cooper, M. L., Maffitt, D. R., Parsons, J. D., Hillier, L. & States, D. J. (1996). Lane tracking software for four-color fluorescence-based electrophoretic gel images. Genome Res 6, 1110-1117.[CrossRef] [Google Scholar]
  17. Dear, S., Durbin, R., Hillier, L., Marth, G., Thierry-Mieg, J. & Mott, R. (1998). Sequence assembly with CAFTOOLS. Genome Res 8, 260-267.[CrossRef] [Google Scholar]
  18. Dujon, B. (1998). European Functional Analysis Network (EUROFAN) and the functional analysis of the Saccharomyces cerevisiae genome. Electrophoresis 19, 617-624.[CrossRef] [Google Scholar]
  19. Ellis, R. E., Sulston, J. E. & Coulson, A. R. (1986). The rDNA of C. elegans: sequence and structure. Nucleic Acids Res 14, 2345-2364.[CrossRef] [Google Scholar]
  20. Ewing, B. & Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8, 186-194. [Google Scholar]
  21. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8, 175-185.[CrossRef] [Google Scholar]
  22. Farwell, M. A., Roberts, M. W. & Rabinowitz, J. C. (1992). The effect of ribosomal protein S1 from Escherichia coli and Micrococcus luteus on protein synthesis in vitro by E. coli and Bacillus subtilis. Mol Microbiol 6, 3375-3383.[CrossRef] [Google Scholar]
  23. Fleischmann, R. D., Adams, M. D., White, O. & 37 other authors (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.[CrossRef] [Google Scholar]
  24. Fraser, C. M. & Fleischmann, R. D. (1997). Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18, 1207-1216.[CrossRef] [Google Scholar]
  25. Gardner, M. J., Tettelin, H., Carucci, D. J. & 22 other authors (1998). Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126–1132. [Google Scholar]
  26. Giddings, M. C., Severin, J., Westphall, M., Wu, J. & Smith, L. M. (1998). A software system for data analysis in automated DNA sequencing. Genome Res 8, 644-665. [Google Scholar]
  27. Gillett, W., Hanks, L., Wong, G. K. S., Yu, J., Lim, R. & Olson, M. V. (1996). Assembly of high-resolution restriction maps based on multiple complete digests of a redundant set of overlapping clones. Genomics 33, 389-408.[CrossRef] [Google Scholar]
  28. Glaser, P., Kunst, F., Arnaud, M. & 14 other authors (1993).Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325 degrees to 333 degrees. Mol Microbiol 10, 371–384.[CrossRef] [Google Scholar]
  29. Goffeau, A. & others (1997). The yeast genome directory. Nature 387 (suppl.), 5–105. [Google Scholar]
  30. Gordon, D., Abajian, C. & Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Res 8, 195-202.[CrossRef] [Google Scholar]
  31. Green, P. (1997). Against a whole-genome shotgun. Genome Res 7, 410-417. [Google Scholar]
  32. Gregory, S., Soderlund, C. & Coulson, A. (1997). Contig assembly by fingerprinting. In Genome Mapping:A Practical Approach, pp. 227-254. Edited by P. Dear. Oxford: Oxford University Press.
  33. Haas, S., Vingron, M., Poustka, A. & Wiemann, S. (1998). Primer design for large scale sequencing. Nucleic Acids Res 26, 3006-3012.[CrossRef] [Google Scholar]
  34. Heiner, C. R., Hunkapiller, K. L., Chen, S. M., Glass, J. I. & Chen, E. Y. (1998). Sequencing multimegabase-template DNA with BigDye terminator chemistry. PCR Methods Appl 8, 557-561. [Google Scholar]
  35. Huang, X. (1996). An improved sequence assembly program. Genomics 33, 21-31.[CrossRef] [Google Scholar]
  36. Isono, K. & Isono, S. (1976). Lack of ribosomal protein S1 in Bacillus stearothermophilus. Proc Natl Acad Sci USA 73, 767-770.[CrossRef] [Google Scholar]
  37. Kececioglu, J. & Myers, E. (1995). Combinatorial algorithms for DNA sequence assembly. Algorithmica 13, 7-51.[CrossRef] [Google Scholar]
  38. Kim, U. J., Shizuya, H., de Jong, P. J., Birren, B. & Simon, M. I. (1992). Stable propagation of cosmid-sized human DNA inserts in an F factor based vector. Nucleic Acids Res 20, 1083-1085.[CrossRef] [Google Scholar]
  39. Kim, U. J., Birren, B. W., Slepak, T., Mancino, V., Boysen, C., Kang, H. L., Simon, M. I. & Shizuya, H. (1996). Construction and characterization of a human bacterial artificial chromosome library. Genomics 34, 213-218.[CrossRef] [Google Scholar]
  40. Klenk, H. P., Clayton, R. A., Tomb, J. F. & 48 other authors (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364–370.[CrossRef] [Google Scholar]
  41. Korch, C. (1987). Cross index for improving cloning selectivity by partially filling in 5′-extensions of DNA produced by type II restriction endonucleases. Nucleic Acids Res 15, 3199-3220.[CrossRef] [Google Scholar]
  42. Kunst, F., Ogasawara, N., Moszer, I. & 148 other authors (1997). The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249–256.[CrossRef] [Google Scholar]
  43. Kurland, C. G. & Dong, H. (1996). Bacterial growth inhibition by overproduction of protein. Mol Microbiol 21, 1-4.[CrossRef] [Google Scholar]
  44. Lander, E. S. & Waterman, M. S. (1988). Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2, 231-239.[CrossRef] [Google Scholar]
  45. Li, P., Kupfer, K. C., Davies, C. J., Burbee, D., Evans, G. A. & Garner, H. R. (1997). PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40, 476-485.[CrossRef] [Google Scholar]
  46. Luo, Y., Glisson, J. R., Jackwood, M. W., Hancock, R. E., Bains, M., Cheng, I. H. & Wang, C. (1997). Cloning and characterization of the major outer membrane protein gene (ompH) of Pasteurella multocida X-73. J Bacteriol 179, 7856-7864. [Google Scholar]
  47. McMurray, A. A., Sulston, J. E. & Quail, M. A. (1998). Short-insert libraries as a method of problem solving in genome sequencing. Genome Res 8, 562-566. [Google Scholar]
  48. Miller, M. J. & Powell, J. I. (1994). A quantitative comparison of DNA sequence assembly programs. J Comput Biol 1, 257-269.[CrossRef] [Google Scholar]
  49. Nelson, K. E., Clayton, R. A., Gill, S. R. & 24 other authors (1999). Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329. [Google Scholar]
  50. Offringa, R. & van der Lee, F. (1995). Isolation and characterization of plant genomic DNA sequences via (inverse) PCR amplification. Methods Mol Biol 49, 181-195. [Google Scholar]
  51. Ogasawara, N., Nakai, S. & Yoshikawa, H. (1994). Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin. DNA Res 1, 1-14.[CrossRef] [Google Scholar]
  52. Petit, M. A., Dervyn, E., Rose, M., Entian, K. D., McGovern, S., Ehrlich, S. D. & Bruand, C. (1998). PcrA is an essential DNA helicase of B. subtilis fulfilling functions both in repair and rolling-circle replication. Mol Microbiol 29, 261-273.[CrossRef] [Google Scholar]
  53. Piper, M. B., Bankier, A. T. & Dear, P. H. (1998). A HAPPY map of Cryptosporidium parvum. Genome Res 8, 1299-1307. [Google Scholar]
  54. Prod’hom, G., Lagier, B., Pelicic, V., Hance, A. J., Gicquel, B. & Guilhot, C. (1998). A reliable amplification technique for the characterization of genomic DNA sequences flanking insertion sequences. FEMS Microbiol Lett 158, 75-81.[CrossRef] [Google Scholar]
  55. Ramos-Diaz, M. A. & Ramos, J. L. (1998). Combined physical and genetic map of Pseudomonas putida KT2440 chromosome. J Bacteriol 180, 6352-6363. [Google Scholar]
  56. Redenbach, M., Kieser, H. M., Denapaite, D., Eichner, A., Cullum, J., Kinashi, H. & Hopwood, D. A. (1996). A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol Microbiol 21, 77-96.[CrossRef] [Google Scholar]
  57. Rose, M. & Entian, K. D. (1996). New genes in the 170 degrees region of the Bacillus subtilis genome encode DNA gyrase subunits, a thioredoxin, a xylanase and an amino acid transporter. Microbiology 142, 3097-3101.[CrossRef] [Google Scholar]
  58. Selkov, E., Maltsev, N., Olsen, G. J., Overbeek, R. & Whitman, W. B. (1997). A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197, GC11-26. [Google Scholar]
  59. Shizuya, H., Birren, B., Kim, U. J., Mancino, V., Slepak, T., Tachiiri, Y. & Simon, M. (1992). Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89, 8794-8797.[CrossRef] [Google Scholar]
  60. Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A. & Lukyanov, S. A. (1995). An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23, 1087-1088.[CrossRef] [Google Scholar]
  61. Singh, G. B. & Krawetz, S. A. (1995).cloneplacer: a software tool for simulating contig formation for ordered shotgun sequencing. Genomics 25, 555-558.[CrossRef] [Google Scholar]
  62. Smith, D. R., Doucette-Stamm, L. A., Deloughery, C. & 34 other authors (1997). Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genomics. J Bacteriol 179, 7135–7155. [Google Scholar]
  63. Soderlund, C., Longden, I. & Mott, R. (1997). FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci 13, 523-535. [Google Scholar]
  64. Sorokin, A., Lapidus, A., Capuano, V., Galleron, N., Pujic, P. & Ehrlich, S. D. (1996). A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing. Genome Res 6, 448-453.[CrossRef] [Google Scholar]
  65. Staden, R. (1979). A strategy of DNA sequencing employing computer programs. Nucleic Acids Res 6, 2601-2610.[CrossRef] [Google Scholar]
  66. Staden, R. (1982). Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res 10, 4731-4751.[CrossRef] [Google Scholar]
  67. Sutton, G., White, O., Adams, M. & Kerlavage, A. (1995). TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol 1, 9-19.[CrossRef] [Google Scholar]
  68. Takeshita, S., Sato, M., Toba, M., Masahashi, W. & Hashimoto-Gotoh, T. (1987). High-copy-number and low-copy-number plasmid vectors for lacZ alpha-complementation and chloramphenicol- or kanamycin-resistance selection. Gene 61, 63-74.[CrossRef] [Google Scholar]
  69. Tao, Q. & Zhang, H.-B. (1998). Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res 26, 4901-4909.[CrossRef] [Google Scholar]
  70. Tomb, J. F., White, O., Kerlavage, A. R. & 39 other authors (1997). The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539–547. [Google Scholar]
  71. Umelo, E. & Trust, T. J. (1998). Physical map of the chromosome of Aeromonas salmonicida and genome comparisons between Aeromonas strains. Microbiology 144, 2141-2149.[CrossRef] [Google Scholar]
  72. Weber, J. L. & Myers, E. W. (1997). Human whole-genome shotgun sequencing. Genome Res 7, 401-409. [Google Scholar]
  73. Xu, S. Y. & Fomenkov, A. (1994). Construction of pSC101 derivatives with Camr and Tetr for selection or LacZ′ for blue/white screening. Biotechniques 17, 57. [Google Scholar]
  74. Ze-Ze, L., Tenreiro, R., Brito, L., Santos, M. A. & Paveia, H. (1998). Physical map of the genome of Oenococcus oeni PSU-1 and localization of genetic markers. Microbiology 144, 1145-1156.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-145-10-2625
Loading
/content/journal/micro/10.1099/00221287-145-10-2625
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error