Abstract
In this paper, we study the problem of inferring duplication history of a tandem gene family using the duplication model proposed by Tang et al.. We provide an efficient algorithm for inferring a duplication model for a given set of (gene) sequences by combining a linear-time algorithm, which is for determining whether a rooted tree is associated with a duplication model, with the nearest neighbor interchange operation. Finally, using our proposed method, we derive duplication hypotheses for an exon of a mucin gene MUC5B, a ZNF gene family, and a OR gene family.
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References
M.D. Adams et al. The genome sequence of Drosophila melanogaster. Science 287 (2000), 2185–2195.
G. Benson and L. Dong. Reconstructing the duplication history of a tandem repeat. In Proceedings of the 7th ISMB, 44–53, 1999.
P. Dehal at al.. Human Chromosome 19 and related regions in Mouse: Conservative and lineage-specific evolution. Science 293 (2001), July, 104–111.
J. L. Desseyn et al. Human mucin gene MUC5B, the 10.7-kb large central exon encodes various alternate subdomains resulting in a super-repeat. Structural evidence for a 11p15.5 gene family. J. Biol. Chem 272 (1997), 3168–3178.
J. L. Desseyn et al. Evolutionary history of the 11p15 human mucin gene family. J. Mol Evol. 46 (1998), 102–106.
J. L. Desseyn et al. Evolution of the large secreted gel-forming mucins, Mol. Biol. Evol. 17 (2000), 1175–1184.
J. Felsentein, PHYLIP, version 3.57c, Dept. of Genetics, Univ. of Washington, Seattle.
S. Ho and Y. Kim. Carbohydrate antigens on cancer-associated mucin-like molecules. Semin. Cancer Biol. 2(1991), 389–400.
X. Huang, Multiple Sequence Alignment, http://genome.cs.mtu.edu/map/map.html.
D. Jaitly et al.. Methods for reconstructing the history of tandem repeats and their application to the human genome. To appear on J. Computer and Systems Sciences.
J. Kim et al. Homology-Driven Assembly of a Sequence-Ready Mouse BAC Contig Map Spanning Regions Related to the 46-Mb Gene-Rich Euchromatic Segments of Human Chromosome 19. Genomics 74(2001), 129–141.
M. Li, J Tromp, and L. Zhang. On the nearest neighbor interchange distance between evolutionary trees. Journal of Theoret. Biol. 182(1996), 463–467.
A. Lim and L. Zhang. WebPHYLIP: A web interface to PHYLIP. Bioinformatics 12(1999), 1068–1069.
P. Pigny et al. Genomics 8(1996), 340–352
D. L. Swofford et al. Phylogeny inference. In Molecular Systematic (edited by D.M. Hillis et al. pages 407–514. Sinauer Associate Inc., MA, 1996.
M. Tang, M. Waterman, and S. Yooseph. Zinc finger gene clusters and tandem gene duplication. RECOMB01, 297–304, 2001.
L. Wang, and D. Gusfield. Improved approximation algorithms for tree alignment. J. of Algorithms 25(1997), 255–273, 1997.
L. Wang, T. Jiang, and E. Lawler. Approximation algorithms for tree alignment with a given phylogeny. Algorithmica 16(3), 302–315, 1996.
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© 2002 Springer-Verlag Berlin Heidelberg
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Zhang, L., Ma, B., Wang, L. (2002). Efficient Methods for Inferring Tandem Duplication History. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_8
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DOI: https://doi.org/10.1007/3-540-45784-4_8
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