Related papers: Variations on the Problem of Identifying Spectrum-…
The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…
Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an…
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a valuable tool within the SPRS, revealing much…
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Automatic cover detection -- the task of finding in an audio database all the covers of one or several query tracks -- has long been seen as a challenging theoretical problem in the MIR community and as an acute practical problem for…
Spectral clustering is one of the most popular clustering methods. However, the high computational cost due to the involved eigen-decomposition procedure can immediately hinder its applications in large-scale tasks. In this paper we use…