Abstract
Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics consisting of pieces of multiple other segmental duplications. This complex genomic organization complicates analysis of the evolutionary history of these sequences. Earlier, we introduced a genomic distance, called duplication distance, that computes the most parsimonious way to build a target string by repeatedly copying substrings of a source string. We also showed how to use this distance to describe the formation of segmental duplications according to a two-step model that has been proposed to explain human segmental duplications. Here we describe polynomial-time exact algorithms for several extensions of duplication distance including models that allow certain types of substring deletions and inversions. These extensions will permit more biologically realistic analyses of segmental duplications in genomes.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B., Cedergren, R.: Gene Order Comparisons for Phylogenetic Inference: Evolution of the Mitochondrial Genome. Proc. Natl. Acad. Sci. U.S.A. 89(14), 6575–6579 (1992)
Pevzner, P.: Computational molecular biology: an algorithmic approach. MIT Press, Cambridge (2000)
Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Assignment of Orthologous Genes via Genome Rearrangement. IEEE/ACM Trans. Comp. Biol. Bioinformatics 2(4), 302–315 (2005)
Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic Distances Under Deletions and Insertions. TCS 325(3), 347–360 (2004)
El-Mabrouk, N.: Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 222–234. Springer, Heidelberg (2000)
Zhang, Y., Song, G., Vinar, T., Green, E.D., Siepel, A.C., Miller, W.: Reconstructing the Evolutionary History of Complex Human Gene Clusters. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 29–49. Springer, Heidelberg (2008)
Ma, J., Ratan, A., Raney, B.J., Suh, B.B., Zhang, L., Miller, W., Haussler, D.: Dupcar: Reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology 15(8), 1007–1027 (2008)
Bertrand, D., Lajoie, M., El-Mabrouk, N.: Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes. J. Comp. Biol. 15(8), 1063–1077 (2008)
Chaudhuri, K., Chen, K., Mihaescu, R., Rao, S.: On the Tandem Duplication-Random Loss Model of Genome Rearrangement. In: Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 564–570. ACM, New York (2006)
Elemento, O., Gascuel, O., Lefranc, M.P.: Reconstructing the Duplication History of Tandemly Repeated Genes. Mol. Biol. Evol. 19(3), 278–288 (2002)
Lajoie, M., Bertrand, D., El-Mabrouk, N., Gascuel, O.: Duplication and Inversion History of a Tandemly Repeated Genes Family. J. Comp. Bio. 14(4), 462–478 (2007)
El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM J. Comput. 32(3), 754–792 (2003)
Alekseyev, M.A., Pevzner, P.A.: Whole Genome Duplications and Contracted Breakpoint Graphs. SICOMP 36(6), 1748–1763 (2007)
Bailey, J., Eichler, E.: Primate Segmental Duplications: Crucibles of Evolution, Diversity and Disease. Nat. Rev. Genet. 7, 552–564 (2006)
Kahn, C.L., Raphael, B.J.: Analysis of Segmental Duplications via Duplication Distance. Bioinformatics 24, i133–i138 (2008)
Kahn, C.L., Raphael, B.J.: A Parsimony Approach to Analysis of Human Segmental Duplications. In: Pacific Symposium on Biocomputing, pp. 126–137 (2009)
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
Kahn, C.L., Mozes, S., Raphael, B.J. (2009). Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-04241-6_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04240-9
Online ISBN: 978-3-642-04241-6
eBook Packages: Computer ScienceComputer Science (R0)