Related papers: On Counting Subsequences and Higher-Order Fibonacc…
We study compositions whose parts are colored by subsequences of the Fibonacci numbers. We give explicit bijections between Fibonacci colored compositions and several combinatorial objects, including certain restricted ternary and…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
A decomposition of a natural number n is a sequence of consecutive natural numbers that sums to n. We construct a one-to-one correspondence between the odd factors of a natural number and its decompositions. We study the decompositions by…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Let $F_n$ be the $n$th Fibonacci number. Let $m, n$ be positive integers. Define a sequence $(G(k,n,m))_{k\geq 1}$ by $G(1,n,m) = F^m_n$, and $G(k+1,n,m) = F_{nG(k,n,m)}$ for all $k\geq 1$. We show that $F_n^{k+m-1}\mid G(k,n,m)$ for all…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
A generalization of the well--known Fibonacci sequence is the $k$--Fibonacci sequence with some fixed integer $k\ge 2$. The first $k$ terms of this sequence are $0,\ldots,0,1$, and each term afterwards is the sum of the preceding $k$ terms.…
The Fibonacci sequence is a series of positive integers in which, starting from $0$ and $1$, every number is the sum of two previous numbers, and the limiting ratio of any two consecutive numbers of this sequence is called the golden ratio.…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
Let $S$ be the numerical semigroup generated by three consecutive numbers $a,a+1,a+2$, where $a\in\mathbb{N}$, $a\geq 3$. We describe the elements of $S$ whose factorizations have all the same length, as well as the set of factorizations of…
Motivated by the study of deletion channels, this work presents improved bounds on the number of subsequences obtained from a binary sting X of length n under t deletions. It is known that the number of subsequences in this setting strongly…
The Tribonacci sequence $\mathbb{T}$ is the fixed point of the substitution $\sigma(a,b,c)=(ab,ac,a)$. In this note, we get the explicit expressions of all squares, and then establish the tree structure of the positions of repeated squares…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
The generalized Fibonacci sequences are sequences $\{f_n\}$ which satisfy the recurrence $f_n(s, t) = sf_{n - 1}(s, t) + tf_{n - 2}(s, t)$ ($s, t \in \mathbb{Z}$) with initial conditions $f_0(s, t) = 0$ and $f_1(s, t) = 1$. In a recent…
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…