Introduction to algorithms
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
SIAM Journal on Discrete Mathematics
Reversals and Transpositions Over Finite Alphabets
SIAM Journal on Discrete Mathematics
Interchange Rearrangement: The Element-Cost Model
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
On the cost of interchange rearrangement in strings
ESA'07 Proceedings of the 15th annual European conference on Algorithms
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The contemporary computational biology gives motivation to study dependencies between finite sequences. Primary structures of DNA or proteins are represented by such sequences (also called words or strings). In the paper a linear algorithm, computing the distance between two words, is presented. The model operates with transpositions of single letters. The cost of a single transposition is equal to the distance which transposed letter has to cover. Other papers concerning the model give, as the best known, algorithms of time complexity O(n log n). The complexity of our algorithm is O(nk), where k is the size of the alphabet, and O(n) when the size is fixed.