Efficient algorithms for multichromosomal genome rearrangements

AbstractHannenhalli and Pevzner (36th Annual Symposium on Foundations of Computer Science, Milwaukee, WI, IEEE Computer Soc. Press, Los Alamitos, CA, 1995, p. 581) gave a polynomial time algorithm for computing the minimum number of reversals, translocations, fissions, and fusions, that would transform one multichromosomal genome to another when both have the same set of genes without repeats. We fixed some problems with the construction: (1) They claim it can exhibit such a sequence of steps, but there was a gap in the construction. (2) Their construction had an asymmetry in the number of chromosomes in the two genomes, whereby forward scenarios could have fissions but not fusions.We also improved the speed by combining the algorithm with the algorithm of Bader et al. (J. Comput. Biol. 8 (5) (2001) 483) that computes reversal distances for permutations in linear time