Abstract
We prove that the genome aliquoting problem, the problem of finding a recent polyploid ancestor of a genome, with breakpoint distance can be solved in polynomial time. We propose an aliquoting algorithm that is a 2-approximation for the genome aliquoting problem with double cut and join distance, improving upon the previous best solution to this problem, Feijão and Meidanis’ 4-approximation algorithm.
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
Alekseyev, M.A., Pevzner, P.A.: Whole genome duplications and contracted breakpoint graphs. SIAM Journal on Computing 36(6), 1748–1763 (2007)
Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)
El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM Journal on Computing 32, 754–792 (2003)
Feijão, P., Meidanis, J.: SCJ: a novel rearrangement operation for which sorting, genome median and genome halving problems are easy. In: Salzberg, S.L., Warnow, T. (eds.) Algorithms in Bioinformatics. LNCS, vol. 5724, pp. 85–96. Springer, Heidelberg (2009)
Lovász, L., Plummer, M.D.: Matching Theory. AMS Chelsea Publishing, Providence (2009)
Mixtacki, J.: Genome halving under DCJ revisited. In: Hu, X., Wang, J. (eds.) COCOON 2008. LNCS, vol. 5092, pp. 276–286. Springer, Heidelberg (2008)
Sankoff, D., Blanchette, M.: The median problem for breakpoints in comparative genomics. In: Jiang, T., Lee, D.T. (eds.) COCOON 1997. LNCS, vol. 1276, pp. 251–264. Springer, Heidelberg (1997)
Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. Bioinformatics 10, 120 (2009)
Warren, R., Sankoff, D.: Genome aliquoting with double cut and join. BMC Bioinformatics 10(1), S2 (2009)
Warren, R., Sankoff, D.: Genome halving with double cut and join. Journal of Bioinformatics and Computational Biology 7(2), 357–371 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Warren, R., Sankoff, D. (2010). Genome Aliquoting Revisited. In: Tannier, E. (eds) Comparative Genomics. RECOMB-CG 2010. Lecture Notes in Computer Science(), vol 6398. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16181-0_1
Download citation
DOI: https://doi.org/10.1007/978-3-642-16181-0_1
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16180-3
Online ISBN: 978-3-642-16181-0
eBook Packages: Computer ScienceComputer Science (R0)