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Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an $O(n \log^3 n)$ time algorithm to chain a set of $n$ anchors so that the…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
The Dushnik-Miller dimension of a partially-ordered set $P$ is the smallest $d$ such that one can embed $P$ into a product of $d$ linear orders. We prove that the dimension of the divisibility order on the interval $\{1, \dotsc, n\}$, is…
An optimal binary search tree for an access sequence on elements is a static tree that minimizes the total search cost. Constructing perfectly optimal binary search trees is expensive so the most efficient algorithms construct almost…
The famous Erdos-Heilbronn conjecture plays an important role in the development of additive combinatorics. In 2007 Z. W. Sun made the following further conjecture (which is the linear extension of the Erdos-Heilbronn conjecture): For any…
We describe a general purpose algorithm for counting simple cycles and simple paths of any length $\ell$ on a (weighted di)graph on $N$ vertices and $M$ edges, achieving a time complexity of $O\left(N+M+\big(\ell^\omega+\ell\Delta\big)…
We construct new linear codes with high minimum distance d. In at least 12 cases these codes improve the minimum distance of the previously known best linear codes for fixed parameters n,k. Among these new codes there is an optimal ternary…
Nonlinear complexity, as an important measure for assessing the randomness of sequences, is defined as the length of the shortest feedback shift registers that can generate a given sequence. In this paper, the structure of n-periodic binary…
A rank-select index for a sequence $B=(b_1,\ldots,b_n)$ of $n$ bits is a data structure that, if provided with an operation to access $\Theta(\log n)$ arbitrary consecutive bits of $B$ in constant time (thus $B$ is stored outside of the…
A sequence $\mathbf{A}$ is said to be realizable if satisfies so called sign and Dold conditions. We will say that a sequence almost satisfies the Dold condition if there exists a constant $c\in\mathbb{N}_+$ such that…
Let $s(n)$ be the number of different remainders $n \bmod k$, where $1 \leq k \leq \lfloor n/2 \rfloor$. This rather natural sequence is sequence A283190 in the OEIS and while some basic facts are known, it seems that surprisingly it has…
For a permutation $\omega\in S_n$, Leclerc and Zelevinsky \cite{LZ} introduced a concept of $\omega$-{\em chamber weakly separated collection} of subsets of $\{1,2,...,n\}$ and conjectured that all inclusion-wise maximal collections of this…
An index coding (IC) problem consisting of a server and multiple receivers with different side-information and demand sets can be equivalently represented using a fitting matrix. A scalar linear index code to a given IC problem is a matrix…
Consider the sequence $\mathcal{V}(2,n)$ constructed in a greedy fashion by setting $a_1 = 2$, $a_2 = n$ and defining $a_{m+1}$ as the smallest integer larger than $a_m$ that can be written as the sum of two (not necessarily distinct)…
Nanopore sequencing is a promising technology for DNA sequencing. In this paper, we investigate a specific model of the nanopore sequencer, which takes a $q$-ary sequence of length $n$ as input and outputs a vector of length $n+\ell-1$…
An n-ary k-radius sequence is a finite sequence of elements taken from an alphabet of size n such that any two distinct elements of the alphabet occur within distance k of each other somewhere in the sequence. These sequences were…
For any three element set of positive integers, $\{a,b,n\}$, with $a<b<n$, $n$ sufficiently large and $\gcd(a,b)=1$, we find the least $\alpha$ such that given any real numbers $t_1$, $t_2$, $t_3$, there is a real number $x$ such that…
We introduce a variant of de Bruijn words that we call perfect necklaces. Fix a finite alphabet. Recall that a word is a finite sequence of symbols in the alphabet and a circular word, or necklace, is the equivalence class of a word under…
We give a short and self-contained argument that shows that, for any positive integers $t$ and $n$ with $t =O\Bigl(\frac{n}{\log n}\Bigr)$, the number $\alpha([t]^n)$ of antichains of the poset $[t]^n$ is at most…
In this paper, we study the well extension of strict(irreflective) partial well orderings. We first prove that any partially well-ordered structure <A, R> can be extended to a well-ordered one. Then we prove that every linear extension of…