Pan genome analysis
Pan-genome Analysis, Visualization and Exploration
... for pan- genome analysis applicable to a wide range of bacterial species, we have developed panX software that combines graph-based approach and phylogeny-based post-processing for rapid iden- ...
102
HUPAN: a pan genome analysis pipeline for human genomes
... for pan-genome ...this analysis could be extended to other populations to capture the glo- bal genetic variations and also various tumors to explore the dynamic variations of cancer ...
11
BPGA- an ultra-fast pan-genome analysis pipeline
... ultra-fast pan-genome analysis pipeline Narendrakumar ...few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic ...resolution. ...
10
Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes
... Conclusions Pan-genome analysis of eukaryotes has become more common, but many of the available software for pan-genome analysis are intended for use with prokaryote ...species ...
15
Pan genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia
... Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia Zhemin Zhou, 1, * Inge Lundstrøm, 2 Alicia Tran-Dien, 3 ...
20
Genome and pan-genome analysis to classify emerging bacteria
... detailed analysis made it possible to select successively the 70 then the 18 most appropriate culture conditions in order to explore the greatest possible diversity for each ...
9
panX: pan-genome analysis and exploration
... isolates––the pan-genome––is often many times larger than the genome of individual ...Custom pan-genomes can be visualized either using a web server or by serving panX locally as a ...
12
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
... publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Background Nowadays, next generation sequencers produce vast amounts of DNA sequence information and it is often the ...
17
Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines
... comparative genome analysis thus highlights a high overall similarity among Xcg strains and a high level of variation in TALE effectors suggestive of duplication and subsequent adaptation to distinct ...
17
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.
... a pan-genome of 21,065 ...(core genome MLST) V2 consists of that subset of 3,002 loci from the wgMLST scheme which met the following conditions for the 3,144 rMLST STs in ...that genome, and ...
21
Pan-genome Analysis of Ancient and Modern <em>Salmonella enterica</em> Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
... a pan-genome of 21,065 ...(core genome MLST) V2 consists of that subset of 3,002 loci from the wgMLST scheme which met the following conditions for the 3,144 rMLST STs in ...that genome, and ...
21
Pan-genome Search and Storage
... III Pan-genome Indexing ...for pan-genome ...the pan-genome of a species, a number far much larger than what is available in most ...(NCBI) Genome database (NCBI, 2017) ...
115
Pan-genome analyses of model fungal species
... archaeal pan- genomes, little dedicated pan-genome software exists for eukaryote ...of analysis, bespoke gene model prediction followed by pan-genome construc- tion using PanOCT ...
23
A novel method of consensus pan chromosome assembly and large scale comparative analysis reveal the highly flexible pan genome of Acinetobacter baumannii
... our pan-genome ortholog clustering tool, PanOCT ...a pan-genome analysis of 249 publicly available ...pre-assigned genome reference and identified both invariant (core) and ...
28
Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity
... our pan-genome analysis of ...core genome, whereas other extracellular proteins and exopolysaccharides are highly variable, occurring in only a limited number of ...core genome of the ...
19
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
... 20. Baier U, Beller T, Ohlebusch E. Graphical pan-genome analysis with com- pressed suffix trees and the Burrows–Wheeler transform. Bioinformatics. 2016;32(4):497–504. 21. Crusoe MR, Alameldin HF, ...
9
Pan-parastagonospora comparative genome analysis-effector prediction and genome evolution
... fungal pan-genome study involving Parastagonospora ...the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and ...the pan- genomic comparative ...
15
The cancer genome atlas pan-cancer analysis project.pdf
... 12 Genome Data Analysis Center: Gordon Saksena 16 , Scott L Carter 16 , Kristian Cibulskis 16 , Lynda Chin 16,22 , Jianhua Zhang 22 , Gad Getz 16,41,42 , Huyen Dinh 12 , Harsha Vardhan Doddapaneni 12 , ...
8
A Pan HIV Strategy for Complete Genome Sequencing
... and genome coverage (from 28% to 54%), pre- sumably by decreasing human background nucleic acid, while a postextraction DNase treatment was often detrimental ...higher genome cov- ...90% genome ...
15
Evolution of the core and pan genome of Streptococcus: positive selection, recombination, and genome composition
... core- genome was particularly evident in the analysis of the differ- ent species within the genus Streptococcus, and it occurred disproportionately in certain lineages, as well as biochemical ...selection ...
17