On the complexity of finding gapped motifs

TL;DR

This paper investigates the computational complexity involved in identifying gapped motifs within biological sequences, providing insights into the algorithmic challenges and theoretical limits of motif discovery.

Contribution

It offers a new complexity analysis of gapped motif finding problems, highlighting their computational hardness and proposing potential directions for efficient algorithms.

Findings

Gapped motif finding is computationally hard in general.

Certain restricted cases admit polynomial-time algorithms.

Theoretical bounds inform future algorithm development.

Abstract

This paper has been withdrawn by the corresponding author because the newest version is now published in Journal of Discrete Algorithms.