Abstract
Recently, several studies taking into account the ability for a gene to be absent or to have some copies in genomes have been proposed, as the examplar distance [6,11] or the gene matching computation between two genomes [3,10]. In this paper, we study the time complexity of the conserved interval distance computation considering duplicated genes using both those two strategies.
This work was partially supported by the French-Italian PAI Galileo project number 08484VH
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
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)
Blanchette, M., Kunisawa, T., Sankoff, D.: Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49(2), 193–203 (1999)
Blin, G., Chauve, C., Fertin, G.: The breakpoints distance for signed sequences. In: Actes de CompBioNets 2004. Texts in Algorithms, vol. 3, pp. 3–16. KCL Publications (2004)
Bourque, G., Pevzner, P.A.: Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res. 12(1), 26–36 (2002)
Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse and rat genomes. Genome Res 14(4), 507–516 (2004)
Bryant, D.: The complexity of calculating exemplar distances. In: Sankoff, D., Nadeau, J. (eds.) Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pp. 207–212. Kluwer Acad. Pub., Dordrecht (2000)
Garey, M., Johnson, D.: Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, New York (1979)
Gascuel, O. (ed.): Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford (2004) (to appear)
Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic distances under deletions and inversions. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 537–547. Springer, Heidelberg (2003)
Moret, B.M.E., Siepel, A.C., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 521–536. Springer, Heidelberg (2002)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Swenson, K.M., Marron, M., Earnest-DeYoung, J.E., Moret, B.M.E.: Approximating the true evolutionary distance between two genomes. Technical Report TR-CS2004-15, Department of Computer Science, University of New Mexico (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Blin, G., Rizzi, R. (2005). Conserved Interval Distance Computation Between Non-trivial Genomes. In: Wang, L. (eds) Computing and Combinatorics. COCOON 2005. Lecture Notes in Computer Science, vol 3595. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11533719_5
Download citation
DOI: https://doi.org/10.1007/11533719_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28061-3
Online ISBN: 978-3-540-31806-4
eBook Packages: Computer ScienceComputer Science (R0)