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Comparing methods for constructing and representing human pangenome graphs [PDF]
, 2023 International audienceBackground As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses.
Dufresne, Yoann +3 more
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The Ecology and Evolution of Pangenomes [PDF]
Current Biology, 2019 Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept.
Brockhurst, M.A. +5 more
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TARGET-MAGs-vs-INDEX-MAGs-PANGENOME [PDF]
, 2020 This data pack is suitable for anvi'o v6.1 or later.This dataset contains anvi'o files for the pangenome shown in Figure 3B of Miyoshi and Miyoshi et al. (2020).To visualize this pangenome interactively please run,anvi-display-pan -p TARGET-MAGs-vs-INDEX-
A. Murat Eren (696829)
core +1 more source
Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics [PDF]
, 2020 AbstractWith the recent technological advancement in cultivation-independent high-throughput sequencing, metagenomes have tremendously improved our ability to characterize the genomic contents of the whole microbial communities. In this chapter, we argue the notion of pangenome can be applied beyond the available genome sequences by leveraging ...
Bing Ma, Michael France, Jacques Ravel
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Challenges in prokaryote pangenomics
Microbial Genomics, 2023 Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche.
Gerry Tonkin-Hill +2 more
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, 2020 This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded.
Tettelin, Hervé, Medini, Duccio
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MAG-01-vs-18-ISOLATES-PANGENOME [PDF]
, 2020 This data pack is suitable for anvi'o v6.1 or later.This dataset contains anvi'o files for the pangenome shown in Figure 3C of Miyoshi and Miyoshi et al.
A. Murat Eren (696829)
core +1 more source
Towards plant pangenomics [PDF]
Plant Biotechnology Journal, 2015 SummaryAs an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of ...
Golicz, Agnieszka A. +2 more
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Pangenome rarefaction curves for the accessory compartment of each ST pangenome. [PDF]
, 2023 Pangenome rarefaction curves for the accessory compartment of each ST pangenome.
Ian-Ling Yu (16559799) +7 more
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Pangenomic genotyping with the marker array
Algorithms for Molecular Biology, 2022 Abstract We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array.
Taher Mun +2 more
openaire +6 more sources