Results 101 to 110 of about 1,556 (147)

Efficient indexing and querying of annotations in a pangenome graph

Abstract The current reference genome is the backbone of diverse and rich annotations. Simple text formats, like VCF or BED, have been widely adopted and helped the critical exchange of genomic information. There is a dire need for tools and formats enabling pangenomic annotation to facilitate such enrichment of pangenomic references ...
Adam M. Novak, Dickson Chung, Glenn Hickey, Sarah Djebali, Toshiyuki T. Yokoyama, Erik Garrison, Giuseppe Narzisi, Benedict Paten, Jean Monlong   +8 more
openaire   +2 more sources

Homology-based perspective on pangenome graphs

Abstract Pangenome graphs conveniently represent genetic variation within a population. Several types of such graphs have been proposed, with varying properties and potential applications. Among them, variation graphs (VGs) seem best suited to replace reference genomes in sequencing data processing, while whole genome alignments (WGAs ...
Anna Lisiecka, Agnieszka Kowalewska, Norbert Dojer   +2 more
openaire   +1 more source

A novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification

BioData Mining
Viral species classification is crucial for understanding viral evolution, epidemiology, and developing effective diagnostics and treatments. Traditional methods often rely on sequence similarity, which can be challenging for rapidly evolving viruses ...
Fabio Cumbo, Kabir Dhillon, Jayadev Joshi, Davide Chicco, Sercan Aygun, Daniel Blankenberg   +5 more
doaj   +1 more source

TEvarSim: A genome simulator for transposable element (TE) variants.

PLoS Computational Biology
Transposable element (TE) variants, the presence or absence of TE sequences such as LINE-1, Alu, SVA, and endogenous retroviruses, are a major source of genomic diversity and play critical roles in human health, evolution, and disease.
Jian Miao, Dawei Li
doaj   +1 more source

Panacus: fast and exact pangenome growth and core size estimation [PDF]

Parmigiani L, Garrison E, Stoye J, Marschall T, Doerr D. Panacus: fast and exact pangenome growth and core size estimation. Bioinformatics. 2024.**Abstract** **Motivation** Using a single linear reference genome ...
Garrison, Erik, Marschall, Tobias, Doerr, Daniel, Stoye, Jens ; https://orcid.org/, Parmigiani, Luca   +4 more
core   +1 more source

Data structures and algorithms for read mapping to pangenome graphs [PDF]

The human reference genome is one of the most important foundational resources in biological research but its utility as a reference for all people is limited due to its lack of diversity.Pangenomes are an alternative representation of genomes that ...
Chang, Xian Hui
core  

Sequence Flow: interactive web application for visualizing partial order alignments

BMC Genomics
Background Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function.
Krzysztof Zdąbłasz, Anna Lisiecka, Norbert Dojer   +2 more
doaj   +1 more source

Establishment of pangenome graphs for the analysis and monitoring of fungal plant pathogen populations [PDF]

International audienceThe assembly of whole genomes by long-read sequencing has enabled the collection of resolved telomere-to-telomere (T2T) haplotypes, encouraging genome-wide approaches to study structural variations.
Loth, Antoine, Duvaux, Ludovic, MARCEL, Thierry, Marcel, Thierry, C, Feurtey, Alice, Genissel, Anne, Lapalu, Nicolas, Lebrun, Marc-Henri, Legeai, Fabrice, Gladieux, Pierre, Fournier, Elisabeth, Lorrain, Cécile   +11 more
core   +1 more source

Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies

GigaScience
Abstract Background Pangenomes are crucial for understanding species-wide genetic diversity, delineating core and variable genes. This study compares 3 key pangenome graph assembly pipelines: Minigraph, PGGB, and Minigraph-Cactus, using publicly available Sorghum data.
Venkataramana Kopalli, Kübra Arslan, Noemia Morales-Díaz, Silvia F Zanini, Agnieszka A Golicz   +4 more
openaire   +2 more sources

Plant graph-based pangenomics: techniques, applications, and challenges

aBIOTECH
Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies in plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating the molecular breeding of crops. Conventional methods for genomic analysis typically rely on small variants, such as SNPs and indels,
Ze-Zhen Du, Jia-Bao He, Wen-Biao Jiao
openaire   +2 more sources