Publications

Abstract : Transforming strings by exchanging elements at bounded distance is applicable in fields like molecular biology, pattern recognition and music theory. A reversal of length two at position i is denoted by (i i+1). When it is applied to π, where π = π 1,π 2, π 3,..., π i ,π i∈+∈1, π n , it transforms π to π′, where π′ = π 1,π 2, π 3,..., π i∈-∈1,π i∈+∈1, π i , π i∈+∈1, ..., π n . We call this operation an adjacent swap. We study the problem of computing the minimum number of adjacent swaps needed to transform one string of size n into another compatible string over an alphabet σ of size k, i.e. adjacent swap distance problem. O(nlog 2 n) time complexity algorithms are known for adjacent swap distance. We give an algorithm with O(nk) time for both signed and unsigned versions of this problem where k is the number of symbols. We also give an algorithm with O(nk) time for transforming signed strings with reversals of length up to 2, i.e. reversals of length 1 or 2. © 2008 Springer-Verlag Berlin Heidelberg.