Results 271 to 280 of about 141,521 (289)

Exploring Frequented Regions in Pan-Genomic Graphs

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications of
Alan M. Cleary, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, Brendan Mumey   +4 more
openaire   +2 more sources

Building Ancestral Recombination Graphs for Whole Genomes

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017
We propose a heuristic algorithm, called ARG4WG, to build plausible ancestral recombination graphs (ARGs) from thousands of whole genome samples. By using the longest shared end for recombination inference, ARG4WG constructs ARGs with small numbers of recombination events that perform well in association mapping on genome-wide association studies.
Thao Thi Phuong Nguyen, Le Sy Vinh, Ho Bich Hai, Si Quang Le   +3 more
openaire   +2 more sources

A Graph Representation of Viral Genomes

2021
The best way for researchers in the biology field to understand how viruses mutate, especially during the COVID-19 pandemic, is to compare the different genomes. Our project’s goal was to create software that visualized the comparisons to support this endeavor.
Ambrose, Michele, Fisher, Jake, Hubert, Jared, Pompeii, Drew, Turner, Caroline   +4 more
openaire   +1 more source

Genome Graphs.

Whole-genome shotgun sequencing is an experimental technique used for obtaining information about a genome’s sequence, whereby it is broken up into many short (possibly overlapping) segments whose sequence is then determined. A long-standing use of sequencing is in genome assembly – the problem of determining the sequence of an unknown genome, which ...
openaire   +1 more source

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

Nature Biotechnology, 2022
Pavel Pevzner, Mikhail Kolmogorov, Andrey Bzikadze   +2 more
exaly  

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

Cell Systems, 2021
Bonnie Berger, Baris Ekim, Rayan Chikhi   +2 more
exaly  

Genome Comparison on Succinct Colored de Bruijn Graphs

Lecture Notes in Computer Science, 2022
Lucas Pansani Ramos, Guilherme P Telles, Louza F A   +2 more
exaly  

Overlap graphs and de Bruijn graphs: data structures for de novogenome assembly in the big data era

Quantitative Biology, 2019
Gianluca Della Vedova, Paola Bonizzoni, Raffaella Rizzi   +2 more
exaly  

How to apply de Bruijn graphs to genome assembly

Nature Biotechnology, 2011
Pavel Pevzner, Phillip E C Compeau, Glenn Tesler   +2 more
exaly  

Graph-based genomic signatures

2014
Ph. D.
openaire   +1 more source