Results 11 to 20 of about 160,024 (241)

Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity

Microbiology Spectrum, 2022
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used ...
Na Liu, Danping Liu, Kexin Li, Songnian Hu, Zilong He   +4 more
doaj   +1 more source

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Genome Biology, 2021
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have ...
Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal   +10 more
doaj   +1 more source

First Steps in the Analysis of Prokaryotic Pan-Genomes

Bioinformatics and Biology Insights, 2020
Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes.
Sávio Souza Costa, Luís Carlos Guimarães, Artur Silva, Siomar Castro Soares, Rafael Azevedo Baraúna   +4 more
doaj   +1 more source

Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets

Frontiers in Microbiology, 2018
Corallococcus is an abundant genus of predatory soil myxobacteria, containing two species, C. coralloides (for which a genome sequence is available) and C. exiguus.
Paul G. Livingstone, Russell M. Morphew, David E. Whitworth   +2 more
doaj   +1 more source

Graph-based pan-genome analysis reveals diversity of structural variations in native and commercial chicken [PDF]

Frontiers of Agricultural Science and Engineering
Chickens are one of the most important domesticated animals, serving as an important protein source. Studying genetic variations in chickens to enhance their production performance is of great potential value.
Yiming WANG, Zijia NI, Yinhua HUANG
doaj   +1 more source

PGAweb: A Web Server for Bacterial Pan-Genome Analysis

Frontiers in Microbiology, 2018
An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species.
Xinyu Chen, Yadong Zhang, Yadong Zhang, Yadong Zhang, Zhewen Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun, Ming Yang, Jinyue Wang, Jinyue Wang, Jinyue Wang, Qian Liu, Qian Liu, Baohua Zhang, Baohua Zhang, Meili Chen, Meili Chen, Jun Yu, Jun Yu, Jiayan Wu, Zhong Jin, Zhong Jin, Jingfa Xiao, Jingfa Xiao, Jingfa Xiao   +25 more
doaj   +1 more source

Reference-agnostic representation and visualization of pan-genomes

BMC Bioinformatics, 2021
Background The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.
Qihua Liang, Stefano Lonardi
doaj   +1 more source

Genomic characterization of Campylobacter jejuni strain M1. [PDF]

PLoS ONE, 2010
Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C.
Carsten Friis, Trudy M Wassenaar, Muhammad A Javed, Lars Snipen, Karin Lagesen, Peter F Hallin, Diane G Newell, Monique Toszeghy, Anne Ridley, Georgina Manning, David W Ussery   +10 more
doaj   +1 more source

Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

Frontiers in Microbiology, 2019
For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified,
Sang-Cheol Park, Kihyun Lee, Yeong Ouk Kim, Sungho Won, Sungho Won, Sungho Won, Jongsik Chun, Jongsik Chun   +7 more
doaj   +1 more source

Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. [PDF]

PLoS Genetics, 2017
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility.
Laurits Skov, Danish Pan Genome Consortium, Mikkel Heide Schierup   +2 more
doaj   +1 more source