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.
This project was partially funded by Finatec-DF, Fundect-MS and MCT/CNPq.
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References
Almeida, N.F.: Tools for genome comparison. PhD thesis, IC-Unicamp, Campinas-SP, Brazil (2002) (in Portuguese)
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)
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)
Birren, B.: Initiative Fungal Genome. A white paper for fungal comparative genomics, Whitehead Institute MIT Center for Genome (October 2003)
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)
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)
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
Kurapakt, G., Sutter-Crazzorala, C.: International Plant and Animal Genome IX Conference (2001), http://www.intl-pag.org/9/abstracts/W15_03.html
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)
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)
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)
Setubal, J.C., Meidanis, J.: Introduction to computational molecular biology. PWS Publishing Co (1997)
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Telles, G.P., Brigido, M.M., Almeida, N.F., Viana, C.J.M., Anjos, D.A.S., Walter, M.E.M.T. (2005). A Method for Comparing Three Genomes. In: Setubal, J.C., Verjovski-Almeida, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2005. Lecture Notes in Computer Science(), vol 3594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11532323_17
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DOI: https://doi.org/10.1007/11532323_17
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