Related papers: Safe and complete contig assembly via omnitigs
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
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…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
We present an algorithm that enumerates all the perfect matchings in a given bipartite graph G = (V,E). Our algorithm requires a constant amortized time to visit one perfect matching of G, in contrast to the current fastest algorithm,…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
The combined Universal Probability M(D) of strings x in sets D is close to max M({x}) over x in D: their ~logs differ by at most D's information j=I(D:H) about the halting sequence H. Thus if all x have complexity K(x) >k, D carries >i bits…
Practical data structures for the edit-sensitive parsing (ESP) are proposed. Given a string S, its ESP tree is equivalent to a context-free grammar G generating just S, which is represented by a DAG. Using the succinct data structures for…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
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…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Representation learning on temporal interaction graphs (TIG) is to model complex networks with the dynamic evolution of interactions arising in a broad spectrum of problems. Existing dynamic embedding methods on TIG discretely update node…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…