相关论文: Safe and complete contig assembly via omnitigs
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
Motivation: The application of PacBio HiFi and ultra-long ONT reads have achieved huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding software,…
De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
Representing a proof tree by a combinator term that reduces to the tree lets subtle forms of duplication within the tree materialize as duplicated subterms of the combinator term. In a DAG representation of the combinator term these…
Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size…
A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S| that contains a representative of each element in S exactly once as a substring. Despite the many universal cycle constructions known in the…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
The commutator length $cl_G(g)$ of an element $g \in [G,G]$ in the commutator subgroup of a group $G$ is the least number of commutators needed to express $g$ as their product. If $G$ is a non-abelian free groups, then given an integer $n…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Term unification plays an important role in many areas of computer science, especially in those related to logic. The universal mechanism of grammar-based compression for terms, in particular the so-called Singleton Tree Grammars (STG),…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
A module of a graph G is a set of vertices that have the same set of neighbours outside. Modules of a graphs form a so-called partitive family and thereby can be represented by a unique tree MD(G), called the modular decomposition tree.…