1887

Abstract

subtractive/differential genome analysis is a powerful approach for identifying genus- or species-specific genes, or groups of genes that are responsible for a unique phenotype. By this method, one searches for genes present in one group of bacteria and absent in another group. A software package has been developed, named FindTarget, that has a user-friendly web interface to facilitate differential genome analysis. The user chooses the genomes to compare, the similarity criteria and the thresholds to decide if a gene has a counterpart in another genome. The searches are based on BLASTP comparisons of proteomes. FindTarget also includes access to sequences, coloured multiple alignments, phylogenetic trees of conserved proteins and links to public annotated databases which provide a means for validation of the results. To illustrate this approach, a FindTarget search for genes putatively involved in the specificity of cell envelope synthesis of Gram-negative bacteria is presented. The results show that most of the identified genes are clearly involved in cell wall processes, underlining the power of such an approach in general and that of FindTarget in particular.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-147-10-2643
2001-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/147/10/1472643a.html?itemId=/content/journal/micro/10.1099/00221287-147-10-2643&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. Brown N. P., Leroy C., Sander C. 1998; MView: a web-compatible database search or multiple alignment viewer. Bioinformatics 14:380–381 [CrossRef]
    [Google Scholar]
  3. Bruccoleri R. E., Dougherty T. J., Davison D. B. 1998; Concordance analysis of microbial genomes. Nucleic Acids Res 26:4482–4486 [CrossRef]
    [Google Scholar]
  4. Corpet F. 1988; Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890 [CrossRef]
    [Google Scholar]
  5. Corpet F., Gouzy J., Kahn D. 1999; Browsing protein families via the ‘Rich Family Description’ format. Bioinformatics 15:1020–1027 [CrossRef]
    [Google Scholar]
  6. Fujita Y., Yoshida K., Miwa Y., Yanai N., Nagakawa E., Kasahara Y. 1998; Identification and expression of the Bacillus subtilis fructose-1,6-bisphosphatase gene ( fbp ). J Bacteriol 180:4309–4313
    [Google Scholar]
  7. Huynen M., Dandekar T., Bork P. 1998; Differential genome analysis applied to the species-specific features of Helicobacter pylori . FEBS Lett 426:1–5 [CrossRef]
    [Google Scholar]
  8. Huynen M. A., Diaz-Lazcoz Y., Bork P. 1997; Differential genome display. Trends Genet 13:389–390 [CrossRef]
    [Google Scholar]
  9. Koonin E. V., Mushegian A. R., Bork P. 1996; Non-orthologous gene displacement. Trends Genet 12:334–336 [CrossRef]
    [Google Scholar]
  10. Krause A., Stoye J., Vingron M. 2000; The systers protein sequence cluster set. Nucleic Acids Res 28:270–272 [CrossRef]
    [Google Scholar]
  11. Kriventseva E. V., Fleischmann W., Zdobnov E. M., Apweiler R. 2001; CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res 29:33–36 [CrossRef]
    [Google Scholar]
  12. Neidhart F. C., Ingraham J. L., Schaechter M. 1990 Physiology of the Bacterial Cell Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  13. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444–2448 [CrossRef]
    [Google Scholar]
  14. Perriere G., Duret L., Gouy M. 2000; hobacgen: database system for comparative genomics in bacteria. Genome Res 10:379–385 [CrossRef]
    [Google Scholar]
  15. Sekowska A., Bertin P., Danchin A. 1998; Characterization of polyamine synthesis pathway in Bacillus subtilis 168. Mol Microbiol 29:851–858 [CrossRef]
    [Google Scholar]
  16. Tatusov R. L., Natale D. A., Garkavtsev I. V. 7 other authors 2001; The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28 [CrossRef]
    [Google Scholar]
  17. Tatusova T. A., Madden T. L. 1999; blast 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250 [CrossRef]
    [Google Scholar]
  18. Wall L., Christiansen T., Schwartz R. L. 1996 Programming Perl , 2nd edition. Sebastopol: O’Reilly & Associates;
    [Google Scholar]
  19. Yona G., Linial N., Linial M. 2000; ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res 28:49–55 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-147-10-2643
Loading
/content/journal/micro/10.1099/00221287-147-10-2643
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