Arc-preserving subsequences of arc-annotated sequences

TL;DR

This paper investigates the computational complexity of the longest arc-preserving common subsequence problem in arc-annotated sequences, establishing NP-completeness results for various structural and alphabet constraints.

Contribution

It proves NP-completeness of the decision versions of the longest arc-preserving subsequence problem for different arc structures and alphabet sizes, advancing understanding of its computational difficulty.

Findings

NP-complete for fixed alphabet size 2 with crossing and chain structures

NP-complete for alphabet size 1 with unlimited plain structures

Highlights the computational hardness of arc-preserving subsequence problems

Abstract

Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. The longest arc-preserving common subsequence problem has been introduced as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures. We consider the longest arc preserving common subsequence problem. In particular, we show that the decision version of the 1-{\sc fragment LAPCS(crossing,chain)} and the decision version of the 0-{\sc diagonal LAPCS(crossing,chain)} are {\bf NP}-complete for some fixed alphabet $\Sigma$ such that $|\Sigma| = 2$. Also we show that if $|\Sigma| = 1$, then the decision version of the 1-{\sc fragment LAPCS(unlimited, plain)} and the decision version of the 0-{\sc diagonal LAPCS(unlimited, plain)} are {\bf NP}-complete.