Weighted shortest common supersequence

Authors:
Amihood Amir;Zvi Gotthilf;B. Riva Shalom
Affiliations:
Department of Computer Science, Bar-Ilan University, Ramat-Gan, Israel and Department of Computer Science, Johns Hopkins University, Baltimore, MD;Department of Computer Science, Bar-Ilan University, Ramat-Gan, Israel;Department of Software Engineering, Shenkar College, Ramat-Gan, Israel
Venue:
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Year:
2011

Citing 9
Cited 0

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Abstract

The Shortest Common Supersequence (SCS) is the problem of seeking a shortest possible sequence that contains each of the input sequences as a subsequence. In this paper we consider applying the problem to Position Weight Matrices (PWM). The Position Weight Matrix was introduced as a tool to handle a set of sequences that are not identical, yet, have many local similarities. Such a weighted sequence is a 'statistical image' of this set where we are given the probability of every symbol's occurrence at every text location. We consider two possible definitions of SCS on PWM. For the first, we give a polynomial time algorithm, having two input sequences. For the second, we prove NP-hardness.