Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2004.02338

The Tandem Duplication Distance Problem is hard over bounded alphabets

Ferdinando Cicalese·Nicolò Pilati
View original source ↗Read source document ↗Export metadata ↓

Abstract

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T = AXXB.$ As they appear to be involved in genetic disorders, tandem duplications are widely studied in computational biology. Also, tandem duplication mechanisms have been recently studied in different contexts, from formal languages, to information theory, to error-correcting codes for DNA storage systems. The problem of determining the complexity of computing the tandem duplication distance between two given strings was proposed by [Leupold et al., 2004] and, very recently, it was shown to be NP-hard for the case of unbounded alphabets [Lafond et al., STACS2020]. In this paper, we significantly improve this result and show that the tandem duplication distance problem is NP-hard already for the case of strings over an alphabet of size $\leq 5.$ We also study some special classes of strings were it is possible to give linear time solutions to the existence problem: given strings $S$ and $T$ over the same alphabet, decide whether there exists a sequence of duplications converting $S$ into $T$. A polynomial time algorithm that solves the existence problem was only known for the case of the binary alphabet.

Explore related subjects

cs.CCcs.DScs.FL

Keep this discovery

BibTeXRIS

Ferdinando Cicalese, Nicolò Pilati. 2020-04-05. The Tandem Duplication Distance Problem is hard over bounded alphabets. https://arxiv.org/abs/2004.02338

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

The Computational Complexity of Holant Problems on 4-regular Graphs from the Stable Subgroup Sequence of $SL(2,\mathbb{C})$

The Holant framework provides a general setting for studying counting problems and includes graph homomorphisms (\#GH) and counting constraint satisfaction problems (\#CSP) as special cases. Over the past twenty years, a series of computational complexity dichotomies have been established for Holant problems, but the classification for complex-valued signatures is still open. The main obstacle is the case in which all signatures have even arity. In this paper, we establish a dichotomy for Holant problems with a complex-valued 4-ary signature, which is a key base case for the full classification of Holant problems. We present a new strategy by introducing Schur's theorem, the classification of finite subgroups of $\mathrm{SL}(2,\mathbb{C})$ and stable subgroup sequences into the proof. These new techniques are of independent interest.

cs.CC↗
arXiv2026

Topology inside NC$^1$

We show that ACC$^0$ is precisely what can be computed with constant-width circuits of polynomial size and polylogarithmic genus. This extends a characterization given by Hansen, showing that planar constant-width circuits also characterize ACC$^0$. Thus polylogarithmic genus provides no additional computational power in this model. We consider other generalizations of planarity, including crossing number and thickness. We show that constant-width circuits of polynomial size and thickness two already suffice to capture all of NC$^1$.

cs.CC↗