Issue No. 04 - October-December (2007 vol. 4)

ISSN: 1545-5963

pp: 535-543

ABSTRACT

In this paper, we investigate the computational and approximation complexity of the Exemplar Longest Common Subsequence of a set of sequences (ELCS problem), a generalization of the Longest Common Subsequence problem, where the input sequences are over the union of two disjoint sets of symbols, a set of mandatory symbols and a set of optional symbols. We show that different versions of the problem are APX-hard even for instances with two sequences. Moreover, we show that the related problem of determining the existence of a feasible solution of the Exemplar Longest Common Subsequence of two sequences is NP-hard. On the positive side, we first present an efficient algorithm for the ELCS problem over instances of two sequences where each mandatory symbol can appear in total at most three times in the sequences. Furthermore, we present two fixed-parameter algorithms for the ELCS problem over instances of two sequences where the parameter is the number of mandatory symbols.

INDEX TERMS

Longest common subsequence, comparative genomics, algorithm design and analysis, combinatorial algorithms, analysis of algorithms and problem complexity

CITATION

St?phane Vialette, Paola Bonizzoni, Riccardo Dondi, Gianluca Della Vedova, Guillaume Fertin, Raffaella Rizzi, "Exemplar Longest Common Subsequence",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol. 4, no. , pp. 535-543, October-December 2007, doi:10.1109/TCBB.2007.1066SEARCH