Skip to main content
SpringerLink
Log in
Book cover

German Conference on Bioinformatics

GCB 1996: Bioinformatics pp 178–188Cite as

Visualization and analysis of the complete yeast genome

  • Visualization
  • Conference paper
  • First Online:

  • 183 Accesses

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1278))

Abstract

In April 1996, the complete sequence of the yeast genome has been released. Now, the systematic analysis of an entire eukaryotic genome is possible. To allow for a global view on the genomic data and for the visualization of sequence homologies within a whole genome, the Genomebrowser has been developed. Furthermore, a structural characterization of the yeast proteins using sequence comparison and structure prediction techniques has been performed. The complete sequence of the yeast genome associated with biological information is available through the W W W. In addition, an intranet solution has been developed to allow the detailed inspection of the Yeast Sequence Database. The CD-ROM includes the Genomebrowser, the functional classification of the open reading frames, aligned protein families and other services based on Java applications and the Netscape browser.

This is a preview of subscription content, log in via an institution.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y. Philippsen P., Tettelin H., and Oliver S.G. Life with 6000 Genes. Science, 274:546–567, 1996

    Google Scholar 

  2. Mewes H.W., Gleissner A., Bähr M., and Heumann K. The complete sequence of the yeast genome. In Proceedings of the German Conference on Bioinformatics. Leipzig, Germany, September/ October 1996.

    Google Scholar 

  3. Fleischmann R.D. et al. Whole-genome random sequencing and assembly of haemophilus influenzae Rd. Science, 269:496–512, 1995.

    Google Scholar 

  4. Fraser C.M. et al. The minimal gene complement of mycoplasma genitalium. Science, 270:397–403, 1995.

    Google Scholar 

  5. Bult Carol et al. Complete. genome sequence of the methanogenic archaeon, methanococcus janischii. Science, 273:1058–1073, 1996.

    Google Scholar 

  6. Dujon B. et al. The complete sequence of chromosome XI of saccharomyces cerevisiae. Nature, 396:371–378, 1994.

    Article  Google Scholar 

  7. Lalo D., Stettler S., Mariotte S., Slonimski P., and Thuriaux P. Two yeast chromosomes are related by a fossil duplication of their centromeric regions. Compts Rendus de L'Acad. Sci., 316(4):367–373, 1993.

    Google Scholar 

  8. Heumann K., Harris C., and Mewes H.W. A top-down approach to whole genome visualization. In Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. St. Louis, USA, June 1996.

    Google Scholar 

  9. Johnston M. et al. Complete nucleotide sequence of saccharomyces cerevisiae chromosome VIII. Science, 256:2077–2082, 1994.

    Google Scholar 

  10. Heumann K. and Mewes H.W. The Hashed Position Tree (HPT): A suffix tree variant for large data sets stored on slow mass storage devices. In Proceedings of the Third South American Workshop on String Processing. Recife, Brazil, August 1996.

    Google Scholar 

  11. Mewes H.W. and Heumann K. Genome analysis: Pattern search in biological macromolecules. In Combinatorial Pattern Matching: Sixth Annual Symposium (CPM). Espoo, Finland, July 1995.

    Google Scholar 

  12. Gonnet C., Mark A., and Benner S. Exhaustive matching of the entire protein sequence database. Science, 256:1443–1445, 1992.

    PubMed  Google Scholar 

  13. Lefevere C. and Ikeda J. The positon end-set tree: A small automaton for ward recognition in biological sequences. Comput. Appl. Biosci., 9:343–348, 1993.

    PubMed  Google Scholar 

  14. Bieganski P., Riedl J., and Cartis J.V. Generalized suffix trees for biological sequence data: applications and implementation. In Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences, Vol. V: Biotechnology Computing. IEEE Comput. Soc. Press, 1994.

    Google Scholar 

  15. Ullman J.D. Principles of Database and Knowledge-Base Systems, Vol. I. Computer Science Press, 1988.

    Google Scholar 

  16. Galibert F. et al. Complete nucleotide sequence of saccharomyces cerevisiae chromosome X. EMBO Journal, 15(9):2031–2049, 1996.

    Google Scholar 

  17. Mewes H.W. and Heumann K. Exhaustive analysis of genetic redundancy in S. cerevisiae. Paper submitted.

    Google Scholar 

  18. George D.G., Barker W.C., Mewes H.W., Pfeiffer F., and Tsugita A. The PIRInternational Protein Sequence Database. Nucleic Acids Research, 24(1):17–20, 1996.

    Article  PubMed  Google Scholar 

  19. Bairoch A. and Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement, TREMBL. Nucleic Acids Research, 24(1):21–25, 1996.

    Article  PubMed  Google Scholar 

  20. Lipman D.J. and Pearson W.R. Rapid and sensitive protein similarity searches. Science, 227:1435–1441, 1985.

    PubMed  Google Scholar 

  21. Etzold T. and Argos P. SRS-an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9:49–57, 1993.

    PubMed  Google Scholar 

  22. Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.F., Brice M.D., Rodgers J.R., Kennard 0., Shimanouchi T., and Tasumi M. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535–542, 1977.

    PubMed  Google Scholar 

  23. Frishman D. and Argos P. Knowledge-based secondary structure assignment. Proteins: Structure, Function, and Genetics, 23:566–579, 1995.

    Google Scholar 

  24. Higgins D.G. Thompson J.D. and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673–4680, 1994.

    PubMed  Google Scholar 

  25. Persson B. and Argos P. Prediction of transmembrane segments in proteins utifising multiple sequence alignments. J. Mol. Biol., 237:182–192, 1994.

    Article  PubMed  Google Scholar 

  26. Kanehisa M. Klein P. and DeLisi C. The detection and classification of membranespanning proteins. Biochim. Biophys. Acta, 815:468–476, 1985.

    PubMed  Google Scholar 

  27. Frishman D. and Argos P. Incorporation of long-range interactions in secondary structure prediction from amino acid sequences. Protein Engineering, 9:133–142, 1996.

    PubMed  Google Scholar 

  28. Frishman D. and Argos P. 75% accuracy in protein secondary structure prediction. Proteins: Structure, Function, and Genetics, 1997-in press.

    Google Scholar 

  29. Levitt M. and Chothia C. Structural patterns in globular proteins. Nature, 261:552–558, 1976.

    Article  PubMed  Google Scholar 

  30. Heumann K., Harris C., Kaps A., Liehl S., Maierl A., Pfeiffer F., and Mewes H.W. An integrated services approach to biological sequence databases. In Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism. GBF Braunschweig, 1995.

    Google Scholar 

  31. Mewes H.W. et al. The Yeast CD-ROM. In preparation.

    Google Scholar 

  32. Flanagan D. Java in a Nutshell. O'Reilly & Associates, Inc., 1996.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max-Planck-Institut für Biochemie, MIPS, Am Klopferspitz, D-82152, Martinsried, Germany

    A. Kaps, K. Heumann, D. Frishman, M. Bahr & H. W. Mewes

Authors
  1. A. Kaps
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K. Heumann
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. Frishman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. Bahr
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. H. W. Mewes
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to H. W. Mewes .

Editor information

Ralf Hofestädt Thomas Lengauer Markus Löffler Dietmar Schomburg

Rights and permissions

Reprints and permissions

Copyright information

© 1997 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Kaps, A., Heumann, K., Frishman, D., Bahr, M., Mewes, H.W. (1997). Visualization and analysis of the complete yeast genome. In: Hofestädt, R., Lengauer, T., Löffler, M., Schomburg, D. (eds) Bioinformatics. GCB 1996. Lecture Notes in Computer Science, vol 1278. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0033216

Download citation

  • DOI: https://doi.org/10.1007/BFb0033216

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63370-9

  • Online ISBN: 978-3-540-69524-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation