Related papers: Palindromic Decompositions with Gaps and Errors
Finding the origin of short phrases propagating through the web has been formalized by Leskovec et al. [ACM SIGKDD 2009] as DAG Partitioning: given an arc-weighted directed acyclic graph on $n$ vertices and $m$ arcs, delete arcs with total…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
We consider the problem of inferring an edge-labeled graph from the sequence of edge labels seen in a walk of that graph. It has been known that this problem is solvable in $O(n \log n)$ time when the targets are path or cycle graphs. This…
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…
We study the relation between the palindromic and factor complexity of infinite words. We show that for uniformly recurrent words one has P(n)+P(n+1) \leq \Delta C(n) + 2, for all n \in N. For a large class of words it is a better estimate…
For a string $S$, a palindromic substring $S[i..j]$ is said to be a \emph{shortest unique palindromic substring} ($\mathit{SUPS}$) for an interval $[s, t]$ in $S$, if $S[i..j]$ occurs exactly once in $S$, the interval $[i, j]$ contains $[s,…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Let H be a connected bipartite graph with n nodes and m edges. We give an O(nm) time algorithm to decide whether H is an interval bigraph. The best known algorithm has time complexity O(nm^6(m + n) \log n) and it was developed in 1997 [18].…
Given a graph $G=(V, E)$ and and a proper labeling $f$ from $V$ to $\{1, ..., n\}$, we define $B(f)$ as the maximum absolute difference between $f(u)$ and $f(v)$ where $(u,v)\in E$. The bandwidth of $G$ is the minimum $B(f)$ for all $f$.…
In the constraint programming framework, state-of-the-art static and dynamic decomposition techniques are hard to apply to problems with complete initial constraint graphs. For such problems, we propose a hybrid approach of these techniques…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
Sum-rank Hamming codes are introduced in this work. They are essentially defined as the longest codes (thus of highest information rate) with minimum sum-rank distance at least $ 3 $ (thus one-error-correcting) for a fixed redundancy $ r $,…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
This paper addresses the problem of identifying palindromic factors in texts that include wildcards -- special characters that match all others. These symbols challenge many classical algorithms, as numerous combinatorial properties are not…
A gapped repeat (respectively, palindrome) occurring in a word $w$ is a factor $uvu$ (respectively, $u^Rvu$) of $w$. In such a repeat (palindrome) $u$ is called the arm of the repeat (respectively, palindrome), while $v$ is called the gap.…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…