Genome Rearrangement by the Double Cut and Join Operation
The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a general mix of linear and circular chromosomes. In the general case the menu includes: inversion, translocation, transposition, formation and absorption of circular intermediates, conversion between linear and circular chromosomes, block interchange, fission, and fusion. This chapter discusses the well-known edge graph and its dual, the adjacency graph, recently introduced by Bergeron et al. Step-by-step procedures are given for constructing and manipulating these graphs. Simple algorithms are given in the adjacency graph for computing the minimal DCJ distance between two genomes and finding a minimal sorting; and use of an online tool (Mauve) to generate synteny blocks and apply DCJ is described.
Key WordsGenome rearrangements gene order Mauve synteny inversion reversal transloca-tion transposition block interchange fission fusion
The authors are grateful to David Sankoff for his advice and encouragement; Anne Bergeron for communicating the idea of the adjacency graph in advance of publication; Mike Tsai for his online implementation of the DCJ; and Betty Harris for invaluable logistic support and encouragement. S.Y. thanks Nicholas Chiorazzi for his enthusiasm, encouragement, and support; and A.E.D is supported by NSF grant DBI-0630765.
- 2.Pevzner, P. A. (2000) Computational Molecular Biology: An Algorithmic Approach. MIT Press, Cambridge, MA.Google Scholar
- 4.Bergeron, A., Mixtacki, J., Stoye, J. (2006) A unifying view of genome rearrangements. WABI 2006, 163–173.Google Scholar
- 7.Meidanis, J., Dias, Z. (2001) Genome rearrangements distance by fusion, fission, and transposition is easy. In Proceedings of SPIRE'2001—String Processing and Information Retrieval, Laguna de San Rafael, Chile.Google Scholar
- 9.Bergeron, A., private communication.Google Scholar
- 10.Bafna, V., Pevzner, P.A. (1993) Genome rearrangements and sorting by reversals. In Proceedings of the 34th Annual IEEE Symposium on Foundations of Computer Science, IEEE Press, Los Alamitos, CA.Google Scholar
- 11.Hannenhalli, S., Pevzner, P. A. (1995) Transforming men into mice (polynomial algorithm for genomic distance problem). In Proceedings of the 36th Annual IEEE Symposium on Foundations of Computer Science, Milwaukee, WI.Google Scholar
- 13.Darling, A. E., Treangen, T. J., Zhang, L., et al. (2006) Procrastination leads to efficient filtration for local multiple alignment. Lecture Notes in Bioinformatics. Springer-Verlag, New York.Google Scholar
- 14.Darling, A. E., Treangen, T. J., Messeguer, X., et al. (2007) Analyzing patterns of microbial evolution using the Mauve genome alignment system, in (Bergman, ed.), Comparative Genomics. Humana Press, Totowa, NJ, in press.Google Scholar