Advertisement

A Method for Comparing Three Genomes

  • Guilherme P. Telles
  • Marcelo M. Brigido
  • Nalvo F. Almeida
  • Carlos J. M. Viana
  • Daniel A. S. Anjos
  • Maria Emilia M. T. Walter
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3594)

Abstract

The large amount of data from complete genomes gave rise to the need for computational tools to analyze and compare them. In this work, we propose a method for comparing three genomes simultaneously, at the basic level of their sequences. This comparison can indicate the set of genes shared by genomes, giving interesting clues about the metabolic pathways and proteins related to particular issues. The input for the method is three sets of gene coding sequences or products and the output are the sequences exclusive to each genome, the sequences common to pairs of genomes, and the sequences common to the three genomes. Because each sequence in a genome may be similar to many sequences in the other two genomes, some complicated situations may arise. The main feature of our method is the ability to avoid such situations. We used our method to compare genomes of two pathogenic and five non-pathogenic fungi, and made a biological analysis based on one of these results.

Keywords

Neurospora Crassa Aspergillus Nidulans Biological Analysis Nucleic Acid Research Proper Region 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Almeida, N.F.: Tools for genome comparison. PhD thesis, IC-Unicamp, Campinas-SP, Brazil (2002) (in Portuguese)Google Scholar
  2. 2.
    Altschul, S.F., Madden, T.L., Schäffer, A.A.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389–3402 (1997)CrossRefGoogle Scholar
  3. 3.
    Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., Sonnhammer, E.L.L.: The Pfam protein families database. Nucleic Acids Research 30(1), 276–280 (2002)CrossRefGoogle Scholar
  4. 4.
    Birren, B.: Initiative Fungal Genome. A white paper for fungal comparative genomics, Whitehead Institute MIT Center for Genome (October 2003)Google Scholar
  5. 5.
    Braun, E.L., Halpern, A.L., Nelson, M.A., Natvig, D.O.: Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Research 10, 416–430 (2000)CrossRefGoogle Scholar
  6. 6.
    Delcher, A.L., Kasif, S., Fleischmann, R.D., White, O., Peterson, J., Salzberg, S.L.: Alignment of whole genomes. Nucleic Acids Research 27(11), 2369–2376 (1999)CrossRefGoogle Scholar
  7. 7.
    Kellis, M., Patterson, N., Birren, B., Berger, B., Lander, E.S.: Methods in comparative genomics: genome correspondence, gene identification and motif discovery. Journal of Computational Biology (in press); Special issue dedicated to Proceedings of the 7th International Conference on Research on Computational Biology Google Scholar
  8. 8.
    Kurapakt, G., Sutter-Crazzorala, C.: International Plant and Animal Genome IX Conference (2001), http://www.intl-pag.org/9/abstracts/W15_03.html
  9. 9.
  10. 10.
    Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P., Zhang, H.: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17(2), 149–154 (2001)CrossRefGoogle Scholar
  11. 11.
    Liu, Y., Liu, X.S., Wei, L., Altman, R.B., Batxoglou, S.: Eukariotic regulatory element conservation analysis and identification using comparative genomics. Genome Research 14, 451–458 (2004)CrossRefGoogle Scholar
  12. 12.
    Ramon, A., Muro-Pastor, M.I., Scazzochio, C., Gonzalez, R.: Deletion of the unique gene encoding a typical Histone H1 has no apparent phenotype in Aspergillus nidulans. Molecular Microbiology 35, 223–233 (2000)CrossRefGoogle Scholar
  13. 13.
    Setubal, J.C., Meidanis, J.: Introduction to computational molecular biology. PWS Publishing Co (1997)Google Scholar
  14. 14.
  15. 15.

Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Guilherme P. Telles
    • 1
  • Marcelo M. Brigido
    • 2
  • Nalvo F. Almeida
    • 3
  • Carlos J. M. Viana
    • 3
  • Daniel A. S. Anjos
    • 4
  • Maria Emilia M. T. Walter
    • 4
  1. 1.Institute for Mathematical and Computer SciencesUniversity of São PauloSão CarlosBrazil
  2. 2.Institute of BiologyUniversity of BrasíliaBrasíliaBrazil
  3. 3.Department of Computing and StatisticsFederal University of Mato Grosso do SulCampo GrandeBrazil
  4. 4.Department of Computer ScienceUniversity of BrasíliaBrasíliaBrazil

Personalised recommendations