Abstract
The double cut and join (DCJ) operation, introduced by Yancopoulos, Attie and Friedberg in 2005, allows one to represent most rearrangement events in genomes. However, a DCJ cannot perform an insertion or a deletion and most approaches under this model consider only genomes with the same content and without duplications, including the linear time algorithms to compute the DCJ distance and to find an optimal DCJ sorting sequence. In this work, we compare two genomes with unequal content, but still without duplications, and present a new linear time algorithm to compute the genomic distance, considering DCJ and indel operations. With this method we find preliminary evidence of the occurrence of clusters of deletions in the Rickettsia bacterium.
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
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)
Blanc, G., et al.: Reductive genome evolution from the mother of Rickettsia. PLoS Genetics 3(1), e14 (2007)
Braga, M.D.V., Stoye, J.: The solution space of sorting by DCJ. To appear in Journal of Computational Biology (2010)
Yancopoulos, S., Friedberg, R.: Sorting Genomes with Insertions, Deletions and Duplications by DCJ. In: Nelson, C.E., Vialette, S. (eds.) RECOMB-CG 2008. LNCS (LNBI), vol. 5267, pp. 170–183. Springer, Heidelberg (2008)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)
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
Braga, M.D.V., Willing, E., Stoye, J. (2010). Genomic Distance with DCJ and Indels. In: Moulton, V., Singh, M. (eds) Algorithms in Bioinformatics. WABI 2010. Lecture Notes in Computer Science(), vol 6293. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15294-8_8
Download citation
DOI: https://doi.org/10.1007/978-3-642-15294-8_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-15293-1
Online ISBN: 978-3-642-15294-8
eBook Packages: Computer ScienceComputer Science (R0)