GRSR: A Tool for Deriving Genome Rearrangement Scenarios from Multiple Unichromosomal Genome Sequences

摘要

Sorting genomic permutations by rearrangement operations is a classic problem in studying genome rearrangements. Many tools or algorithms have been proposed for sorting signed genomic permutations [1, 2]. In fact, given a pair of permutations, there are often more than one optimal rearrangement scenarios, especially when the rearrangement distance between this permutation pair is large. And sometimes, for the same pair of permutations, the computed rearrangement scenarios using different tools are not consistent. Hence, how to know whether the calculated scenarios are solid and biologically meaningful becomes an essential task. Up to now, several mechanisms for genome rearrangements have been reported [3, 4]. Statistics analyzes showed that breakpoints are often associated with repetitive elements [5, 6]. There was evidence showing that a reversal can be mediated by a pair of inverted repeats (IRs) [7, 8]. Hence, whether there exist repeats at the breakpoints of rearrangement events may give us a clue on whether the calculated rearrangement scenarios are biologically meaningful.