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Let's denote a complete $m$-ary rooted tree graph of height $n$ as $G$. In scope of this paper we prove the certain relations between the properties of $G$ and the expectation and variance of the distribution of lengths of strings,…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
We consider the problem of upper bounding the number of circular transpositions needed to sort a permutation. It is well known that any permutation can be sorted using at most $n(n-1)/2$ adjacent transpositions. We show that, if we allow…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
We study (symbol-pair) codes for symbol-pair read channels introduced recently by Cassuto and Blaum (2010). A Singleton-type bound on symbol-pair codes is established and infinite families of optimal symbol-pair codes are constructed. These…
The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the…
Many natural language processing (NLP) applications require the computation of similarities between pairs of syntactic or semantic trees. Many researchers have used tree edit distance for this task, but this technique suffers from the…
We give cell-probe bounds for the computation of edit distance, Hamming distance, convolution and longest common subsequence in a stream. In this model, a fixed string of $n$ symbols is given and one $\delta$-bit symbol arrives at a time in…
In two dimensions large N QCD with quarks, defined on the plane, is equivalent to a modified string theory with quarks at the ends and taken in the zero fold sector. The equivalence that was established in 1975 was expressed in the form of…
We consider two independent binary i.i.d. random strings $X$ and $Y$ of equal length $n$ and the optimal alignments according to a symmetric scoring functions only. We decompose the space of scoring functions into five components. Two of…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
Let $n_q(M,d)$ be the minimum length of a $q$-ary code of size $M$ and minimum distance $d$. Bounding $n_q(M,d)$ is a fundamental problem that lies at the heart of coding theory. This work considers a generalization $n^\bx_q(M,d)$ of…
There are at present two known string theories in $(2,2)$ dimensions. One of them is the well known $N=2$ string, and the other one is a more recently constructed $N=1$ spacetime supersymmetric string. They are both based on certain…
We say that a $q$-ary length $n$ code is \emph{non-overlapping} if the set of non-trivial prefixes of codewords and the set of non-trivial suffices of codewords are disjoint. These codes were first studied by Levenshtein in 1964, motivated…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA…