What Makes the Arc-Preserving Subsequence Problem Hard?

Abstract. Given two arc-annotated sequences (S, P) and (T, Q) representing RNA structures, the Arc-Preserving Subsequence (APS) problem asks whether (T, Q) can be obtained from (S, P) by deleting some of its bases (together with their incident arcs, if any). In previous studies [3, 6], this problem has been naturally divided into subproblems reflecting intrinsic complexity of arc structures. We show that APS(Crossing, Plain) is NP-complete, thereby answering an open problem [6]. Furthermore, to get more insight into where actual border of APS hardness is, we refine APS classical subproblems in much the same way as in [11] and give a complete categorization among various restrictions of APS problem complexity.

• Type: Conference
• Year: 2005
• Where: ICCS
• Authors: Guillaume Blin, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
• Keywords: APS Classical Subproblems, APS Hardness, APS Problem Complexity, ICCS 2005