Vol. 7 No. 2 (2004)
Research Article

Annotating the Mycobacterium avium Genome: A Project in Bioinformatics

PDF
  • David D. Shersher,
  • Maksim Kirtsman,
  • Mikael Katz-Lavigne,
  • Marcel A. Behr, MD MSc,
  • Makeda Semret , MD MSc
DOI: https://doi.org/10.26443/mjm.v7i2.383

Published 2004-12-01

Keywords

  • Mycobacterium avium complex,
  • annotation,
  • genomics,
  • BLAST

How to Cite

1.
Shersher DD, Kirtsman M, Katz-Lavigne M, Behr MA, Semret M. Annotating the Mycobacterium avium Genome: A Project in Bioinformatics. McGill J Med [Internet]. 2004 Dec. 1 [cited 2025 Oct. 20];7(2). Available from: https://mjm.mcgill.ca/article/view/383

Copyright (c) 2004 David D. Shersher, Maksim Kirtsman, Mikael Katz-Lavigne, Marcel A. Behr, MD MSc, Makeda Semret , MD MSc

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Crossref
Scopus
Google Scholar
Europe PMC

Abstract

Bioinformatic tools facilitate efficient processing and formatting of experimental data and are becoming essential to research in the biological sciences. Whole genome sequencing projects, combined with DNA microarray technology, have allowed genomic comparisons between and within species of microorganisms. The genome of Mycobacterium avium subsp. avium (MAA) has been sequenced by The Institute for Genomic Research (TIGR), but a final and annotated version has not yet been made available. The goal of this project was to annotate the sequence of MAA as a foundation for microarray-based genomic comparisons. We used software to identify and predict open reading frames (ORFs) present in this organism. The ORFs were then compared to those catalogued in two large, online genetic databases for other microorganisms and matched to homologous sequences, allowing the determination of putative functions for each predicted gene. The genome of MAA was determined to contain 4480 genes, the majority of which are homologous to genes found in other Mycobacterial species.

PDF

Downloads

Download data is not yet available.

References

  1. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry, III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, B. G. Barrell, and . 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
  2. Behr, M. A., M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523.
  3. Mostowy, S., D. Cousins, J. Brinkman, A. Aranaz, and M. A. Behr. 2002. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J.Infect.Dis. 186:74-80.
  4. Kato-Maeda, M., J. T. Rhee, T. R. Gingeras, H. Salamon, J. Drenkow, N. Smittipat, and P. M. Small. 2001. Comparing genomes within the species Mycobacterium tuberculosis. Genome Res. 11:547-554.
  5. El Zaatari, F. A., M. S. Osato, and D. Y. Graham. 2001. Etiology of Crohn's disease: the role of Mycobacterium avium paratuberculosis. Trends Mol.Med. 7:247-252.
  6. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J.Mol.Biol. 215:403-410.
  7. Bannantine, J. P., E. Baechler, Q. Zhang, L. Li, and V. Kapur. 2002. Genome scale comparison of Mycobacterium avium subsp. paratuberculosis with Mycobacterium avium subsp. avium reveals potential diagnostic sequences. J.Clin.Microbiol. 40:1303-1310.
  8. Bannantine, J. P., Q. Zhang, L. L. Li, and V. Kapur. 2003. Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. BMC.Microbiol. 3:10.