Genomic Sorting withLength-Weighted Reversals.pptVIP

Computer Science DepartmentTechnion – Israel Institute of TechnologyGenomic Sorting with Length-Weighted ReversalsRon Y. PinterTechnionSteve SkienaSUNY Stony Brook Genome Rearrangement events duplication translocation reversal (inversion) occur primarily during reproduction allow large-scale genomic comparisons Sorting by Reversals genome represented as a permutation on 1, 2, …, n n = # homologous genes among species assumptions can identify genes genes are distinct operation: reversal of a subsequence (of genes) models inversion (occurs during crossover) one of the permutations can be 1, 2, …, n appropriately relabel others Example 6 reversal in our model (for f(l) = l): cost = 18 Our Model unsigned cost of reversal of subsequence of length l is f(l) total sorting cost (or distance) is f (length(sj)) Cost Functions additive f(x+y) = f(x) + f(y) subadditive f(x+y) f(x) + f(y) superadditive f(x+y) f(x) + f(y) other e.g. bitonic Problems algorithm to sort any permutation worst-case min cost approximate min cost for a given permutation Extremal Costs highly subadditive: e.g. unit cost, f(l) = 1 NP complete [Caprara, ’97] series of approximation ratios: 2, 1.75, 1.375 highly superadditive: f(l) l2 essentially bubblesort Our Results additive cost function specifically f(l) = l QuickSort-like algorithm for worst-case complexity: O(n lg2n) min cost approximation ratio of O(lg2n) MedianEject(a,b) find r maximal blocks of wrong-sided elements with respect to median for lg r do: flip every other pair of blocks of wrong-sided and adjacent blocks move wrong-sided blocks to median boundary reverse left and right blocks Sample Run complexity: O((b-a) lg r) ReversalSort(a,b) MedianEject (a,b); ReversalSort (a, ); ReversalSort ( ,b); Complexity T(n) = 2 ? T ( ) + O(f(n) lg n) O(f(n)lg2n) = O(n lg2n) for f(n)~n Algorithmic Improvements I simplif