An automated system for genome analysis to support microbial whole-genome shotgun sequencing

Bioscience, Biotechnology and Biochemistry

Volumn 64, Issue 3, 2000, Pages 670-673

  Sakiyama, Tokuki ^a   Takami, Hideto ^a   Ogasawara, Naotake ^b   Kuhara, Satoru ^c   Kozuki, Tokio ^d   Doga, Kosuke ^d   Ohyama, Akira ^d   Horikoshi, Koki ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d Mitsui Knowledge Industry Co   (Japan)

Author keywords

Bacillus halodurans C 125; Genome analysis; Software; Whole genome shotgun method

Indexed keywords

ARTICLE; AUTOMATION; BACILLUS; BACTERIAL GENOME; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; HUMAN; INFORMATION PROCESSING; METHODOLOGY;

AUTOMATIC DATA PROCESSING; AUTOMATION; BACILLUS; GENOME, BACTERIAL; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0034150045     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.64.670     Document Type: Article

References (15)

1. Anderson, S., de Bruijn, M. H., Coulson, A. R., Eperon, I. C., Sanger, F., and Young, I. G., Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol., 156, 683-717 (1982).
2. Fleischmann, R. D. Adams, M. D. et al., Whole genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512 (1995).
3. Takami, H. and Horikoshi, K., Reidentification of facultatively alkaliphilic Bacillus sp. C-125 to Bacillus halodurans. Biosci. Biotechnol. Biochem., 63, 943-945 (1999).
4. Takami, H., Nakasone, K., Hirama, C., Takaki, Y., Masui, N., Fuji, F., Nakamura, Y., and Inoue, A., An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125. Extremophiles, 3, 21-28 (1999).
5. Ewing, B., Hillier, L., Wendl, M.C., and Green, P., Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res., 8, 175-185 (1998).
6. Ewing, B. and Green, P., Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res., 8, 186-194 (1998).
7. Smith, T. F. and Waterman, M. S., Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197 (1981).
8. Gotoh, O., An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708 (1982).
9. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J., Basic local alignment search tool. J. Mol. Biol., 215, 403-410 (1990).
10. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402 (1997).
11. Lipman, D. J. and Pearson, W. R., Rapid and sensitive protein similarity searches. Science, 227, 1435-1441 (1985).
12. Wilbur, W. J. and Lipman, D. J., Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA, 80, 726-730 (1983).
13. Takami, H., Nakasone, K., Ogasawara, N., Hirama, C., Nakamura, Y., Masui, N., Fuji, F., Takaki, Y., Inoue, A., and Horikoshi, K., Sequencing of three lambda clones from the genome of alkaliphilic Bacillus sp. strain C-125. Extremophiles, 3, 29-34 (1999).
14. Dear, S. and Staden, R., A standard file format for data from DNA sequencing instruments. DNA Seq., 3, 107-110. (1992).
15. Gordon, D., Abajian, C., and Green, P., Consed: a graphical tool for sequence finishing. Genome Res., 8, 195-202 (1998).