Abstract
Comparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular genomes based on a set of conserved genes. Following this assumption, the common interval appears to be a good candidate. For evidences, we propose herein an approach to compute the common intervals between two circular genomes that takes into account duplications. Its application on a concrete case, comparing E. coli and V. cholerae, is accurate. It indeed emphasizes sets of conserved genes that present high impacts on bacterial functions.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Angibaud, S., Fertin, G., Rusu, I.: On the approximability of comparing genomes with duplicates. In: Nakano, S.-i., Rahman, M. S. (eds.) WALCOM 2008. LNCS, vol. 4921, pp. 34–45. Springer, Heidelberg (2008)
Angibaud, S., Fertin, G., Rusu, I., Vialette, S.: A pseudo-boolean general framework for computing rearrangement distances between genomes with duplicates. Journal of Computational Biology 14(4), 379–393 (2007)
Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)
Berglund, A., Sjölund, E., Ostlund, G., Sonnhammer, E.L.L.: Inparanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36(Database issue), D263–D266 (2008)
Blin, G., Chauve, C., Fertin, G., Rizzi, R., Vialette, S.: Comparing genomes with duplications: A computational complexity point of view. IEEE/ACM Transactions on Computational Biology and Bioinformatics 4(4), 523–534 (2007)
Curtis, T.P., Sloan, W.T.: Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr. Opin. Microbiol. 7(3), 221–226 (2004)
Doolittle, W.F.: Phylogenetic classification and the universal tree. Science 284(5423), 2124–2129 (1999)
Eén, N., Sörensson, N.: Translating pseudo-boolean constraints into SAT. Journal on Satisfiability, Boolean Modeling and Computation 2, 1–26 (2006)
Fullner, K.J., Mekalanos, J.J.: Genetic characterization of a new type IV-a pilus gene cluster found in both classical and El Tor biotypes of Vibrio cholerae. Infect. Immun. 67(3), 1393–1404 (1999)
Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spínola, M.I., Bonavides-Martinez, C., Ingraham, J.: Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35(22), 7577–7590 (2007)
Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., Peralta-Gil, M., Karp, P.D.: Ecocyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33(Database issue), D334–D337 (2005)
Ochman, H., Davalos, L.M.: The nature and dynamics of bacterial genomes. Science 311(5768), 1730–1733 (2006)
Remm, M., Strom, C.E., Sonnhammer, E.L.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Molecular Biology 314, 1041–1052 (2001)
Ruby, E.G., Urbanowski, M., Campbell, J., Dunn, A., Faini, M., Gunsalus, R., Lostroh, P., Lupp, C., McCann, J., Millikan, D., Schaefer, A., Stabb, E., Stevens, A., Visick, K., Whistler, C., Greenberg, E.P.: Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc. Natl. Acad. Sci. USA 102(8), 3004–3009 (2005)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Schrijver, A.: Theory of Linear and Integer Programming. John Wiley and Sons, Chichester (1998)
Tanapongpipat, S., Reid, E., Cole, J.A., Crooke, H.: Transcriptional control and essential roles of the Escherichia coli ccm gene products in formate-dependent nitrite reduction and cytochrome C synthesis. Biochem J. 334(pt. 2), 355–365 (1998)
Tang, J., Moret, B.M.E.: Phylogenetic reconstruction from gene-rearrangement data with unequal gene content. In: Dehne, F., Sack, J.-R., Smid, M. (eds.) WADS 2003. LNCS, vol. 2748, pp. 37–46. Springer, Heidelberg (2003)
Thöny-Meyer, L.: Haem-polypeptide interactions during cytochrome C maturation. Biochim. Biophys. Acta. 1459(2-3), 316–324 (2000)
Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290–309 (2000)
Whitman, W.B., Coleman, D.C., Wiebe, W.J.: Prokaryotes: the unseen majority. Proc. Natl. Acad Sci. USA 95(12), 6578–6583 (1998)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Angibaud, S., Eveillard, D., Fertin, G., Rusu, I. (2009). Comparing Bacterial Genomes by Searching Their Common Intervals. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_12
Download citation
DOI: https://doi.org/10.1007/978-3-642-00727-9_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00726-2
Online ISBN: 978-3-642-00727-9
eBook Packages: Computer ScienceComputer Science (R0)