The Longest Filled Common Subsequence Problem

Mauro Castelli, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis, Marc Herbstritt
2017 Annual Symposium on Combinatorial Pattern Matching  
Inspired by a recent approach for genome reconstruction from incomplete data, we consider a variant of the longest common subsequence problem for the comparison of two sequences, one of which is incomplete, i.e. it has some missing elements. The new combinatorial problem, called Longest Filled Common Subsequence, given two sequences A and B, and a multiset M of symbols missing in B, asks for a sequence B * obtained by inserting the symbols of M into B so that B * induces a common subsequence
more » ... mmon subsequence with A of maximum length. First, we investigate the computational and approximation complexity of the problem and we show that it is NP-hard and APX-hard when A contains at most two occurrences of each symbol. Then, we give a 3 5 −approximation algorithm for the problem. Finally, we present a fixed-parameter algorithm, when the problem is parameterized by the number of symbols inserted in B that "match" symbols of A.
doi:10.4230/lipics.cpm.2017.14 dblp:conf/cpm/CastelliDMZ17 fatcat:mzw2go3jvngtxphnbuk633rdoq