The Genesis of the DCJ Formula
The formula N−(C+I/2) to compute the number of Double-Cut-and-Join operations needed to transform one genome into another is both simple and easy to prove. When it was published, in 2006, we omitted all details on how it was constructed. In this chapter, we will give an elementary treatment on the intuitions and methods underlying the formula, showing that simplicity is sometimes difficult to achieve. We will also prove that this formula is one among an infinite number of candidates, and that the techniques can be applied to other genomic distances.
KeywordsGenome Rearrangement Edit Distance Adjacency Graph Circular Chromosome Linear Chromosome
- 2.Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Proceedings of WABI 2006. LNBI, vol. 4175, pp. 163–173 (2006) Google Scholar
- 3.Dobzhansky, T., Sturtevant, A.H.: Inversions in the chromosomes of drosophila pseudoobscura. Genetics 23(1), 28–64 (1938) Google Scholar
- 5.Feijão, P., Meidanis, J.: Extending the algebraic formalism for genome rearrangements to include linear chromosomes. In: Proceedings of BSB 2012. LNBI, vol. 7409, pp. 13–24 (2012) Google Scholar
- 6.Hannenhalli, S., Pevzner, P.A.: Transforming men into mice (polynomial algorithm for genomic distance problem). In: Proceedings of FOCS 1995, pp. 581–592 (1995) Google Scholar
- 9.Wikipedia: http://en.wikipedia.org/wiki/DNA_repair