1887

Abstract

Techniques drawn from exploratory data analysis, using tools found in the S-Plus statistical software package, have been used to inspect and maintain the and to move towards an automated and community-based means of working on the outline. These techniques can be used to classify sequences from unnamed and uncultured organisms, to visualize errors in the taxonomy or in the curation of the sequences, to suggest emendations to the taxonomy or to the classification of extant species and to complement the visualization of phylogenies based on treeing methods. A dataset of more than 9200 aligned small-subunit rRNA sequences was analysed in the context of the current taxonomic outline. The use of the algorithm in exploring and modifying the taxonomy is illustrated with an example drawn from the family .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02749-0
2004-01-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/1/ijs540007.html?itemId=/content/journal/ijsem/10.1099/ijs.0.02749-0&mimeType=html&fmt=ahah

References

  1. Brown J. R., Koretke K. K. 2000; Universal trees: discovering the archaeal and bacterial legacies. In Applied Microbial Systematics pp  19–55 Edited by Priest F. G., Goodfellow M. Dordrecht: Kluwer;
    [Google Scholar]
  2. Cannone J. J., Subramanian S., Schnare M. N. 11 other authors 2002; The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics 3:2 [CrossRef]
    [Google Scholar]
  3. Eisen M. B., Spellman P. T., Brown P. O., Botstein D. 1998; Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95:14863–14868 [CrossRef]
    [Google Scholar]
  4. Fox G. E., Stackebrandt E., Hespell R. B. 16 other authors 1980; The phylogeny of prokaryotes. Science 209:457–463 [CrossRef]
    [Google Scholar]
  5. Garrity G. M., Lilburn T. G. 2002; Mapping taxonomic space: an overview of the road map to the second edition of Bergey's Manual of Systematic Bacteriology. WFCC Newsl 35:5–15
    [Google Scholar]
  6. Garrity G. M., Johnson K. L., Bell J., Searles D. B. 2002; Taxonomic outline of the procaryotes . Release 3:0 July 2002 http://dx.doi.org/10.1007/bergeysoutline
    [Google Scholar]
  7. Hebert P. D. N., Cywinska A., Ball S. L., deWaard J. R. 2003; Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270:313–321 [CrossRef]
    [Google Scholar]
  8. Jukes T. H., Cantor R. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp  21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  9. Maidak B. L., Cole J. R., Lilburn T. G. 7 other authors 2001; The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174 [CrossRef]
    [Google Scholar]
  10. Sneath P. H. A., Sokal R. R. 1973 Numerical Taxonomy. The Principles and Practice of Numerical Classification San Francisco: W. H. Freeman;
    [Google Scholar]
  11. Swofford D. 2000 PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Sunderland, MA: Sinauer;
    [Google Scholar]
  12. Tekaia F., Lazcano A., Dujon B. 1999; The genomic tree as revealed from whole proteome comparisons. Genome Res 9:550–557
    [Google Scholar]
  13. Tukey J. W. 1977 Exploratory Data Analysis Reading, PA: Addison-Wesley;
    [Google Scholar]
  14. Willems A., Gillis M. 2004 Family Comamonadaceae Willems, De Ley, Gillis and Kersters 1991, 447VP. In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 2 The Proteobacteria , part C, The Betaproteobacteria, the Deltaproteobacteria and the Epsilonproteobacteria Edited by Brenner D. J., Kreig N. P., Staley J. T., Garrity G. M. New York: Springer; (in press
    [Google Scholar]
  15. Wuyts J., Van de Peer Y., De Wachter R. 2001; Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29:5017–5028 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.02749-0
Loading
/content/journal/ijsem/10.1099/ijs.0.02749-0
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