The traditional edit-distance problem is to find the minimum number of insert-character and delete-character (and sometimes change character) operations required to transform one string into another. Here we consider the more general problem of strings being represented by a singly linked list (one character per node) and being able to apply these operations to the pointer associated with a vertex as well as the character associated with the vertex. That is, in O(1) time, not only can characters be inserted or deleted, but also substrings can be moved or deleted. We limit our attention to the ability to move substrings and leave substring deletions for future research. Note that O(1) time substring move operations imply O(1) substring exchange operations as well, a form of transformation that has been of interest in molecular biology. We show that this problem is NP-complete, show that a “recursive” sequence of moves can be simulated with at most a constant factor increase by a non-recursive sequence, and present a polynomial time greedy algorithm for non-recursive moves with a worst-case log factor approximation to optimal. The development of this greedy algorithm shows how to reduce moves of substrings to moves of characters, and how to convert moves with characters to only insert and deletes of characters.
|Title of host publication||Combinatorial Pattern Matching - 13th Annual Symposium, CPM 2002, Proceedings|
|Editors||Alberto Apostolico, Masayuki Takeda|
|Number of pages||14|
|State||Published - 2002|
|Event||13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002 - Fukuoka, Japan|
Duration: 3 Jul 2002 → 5 Jul 2002
|Name||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Conference||13th Annual Symposium on Combinatorial Pattern Matching, CPM 2002|
|Period||3/07/02 → 5/07/02|
Bibliographical notePublisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.