Additional strains for pan-genome analyses
Pan-genome analyses of model fungal species
... species pan-genome datasets based on strain genome assemblies that were available from GenBank at the start of our analy- ...the genome assembly data ...of strains sampled for these ...
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Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway
... 17 strains were consid- erably different from that of ...different strains (Additional file 5: Figure ...these strains was determined according to their genetic characteris- ...baltica ...
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The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract
... Bioinformatics analyses of ATCC 53608 genome The finished ...different analyses, and in addition, results from an automated RAST (Rapid Annotation using Subsystem Technology) [79] annotation were ...
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First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico
... pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess ...All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and ...
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Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits
... comparative pan-genomic analysis of ...core genome and shared virulence factors revealed different cluster groups, which suggested a possible link with the virulence properties and supported the idea that ...
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Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines
... complete genome sequences of three Xcg strains, 8ra, 12-2, and EB08 [21,22], were generated using PacBio long-read ...These strains exhibited strong con- servation in their overall synteny and ...
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Genome-wide analyses of Bacillus amyloliquefaciens strains provide insights into their beneficial role on plants
... Genome-wide Analyses of Bacillus amyloliquefaciens strains Provide Insights into their Beneficial Role on Plants Abstract The innate immunity system of plants provides a basal defence barrier to most ...
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Pan-genome Search and Storage
... making genome sequencing more ...overlapping genome fragments that are erroneous and cover the sequenced genomes ...These genome fragments are assembled based on their overlaps to produce larger ...
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Pan Genome and Comparative Genome Analyses of Propionibacterium acnes Reveal Its Genomic Diversity in the Healthy and Diseased Human Skin Microbiome
... The GENOME Institute at Washington University in ...comparative genome analysis of 82 P. acnes strains, 69 of which were sequenced by our ...acnes pan-genome is open, it is relatively ...
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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- tification of ...
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panX: pan-genome analysis and exploration
... related strains can differ in the presence or ab- sence of many genes, and the total number of dis- tinct genes found in a set of related isolates––the pan-genome––is often many times larger than the ...
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Comparative analyses of Campylobacter concisus strains reveal the genome of the reference strain BAA-1457 is not representative of the species
... concisus strains UNSWCD and BAA-1457, proteins found in both strains but not in another bacterial species may be ideal markers for the detection of this ...two strains were conducted against all ...
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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 ...discovering additional ...
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A Pan HIV Strategy for Complete Genome Sequencing
... proach is an attractive, simple alternative that generally performs better than current unbiased priming methods. All told, we deployed HIV-SMART to obtain 56 novel full- length genomes, including 3 URFs, 3 rare group M ...
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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 ...
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HUPAN: a pan genome analysis pipeline for human genomes
... Supplementary methods). In HUPAN pipeline, we focused on two types of non-reference sequences: fully unaligned sequences and partially unaligned sequences. Fully un- aligned sequences are defined as contigs with no ...
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The cancer genome atlas pan-cancer analysis project.pdf
... rations from passengers? A bird’s-eye view of genomic and epigenomic events yields a ‘fate map’ of the alternative routes to carcinogenesis in a decision tree that spans tissue boundaries 37 . Can molecular subtypes be ...
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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. ...
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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 ...
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Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains
... longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a ...
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