Core and pan genome analysis
Genome and pan-genome analysis to classify emerging bacteria
... of pan-genomic analyses, species can be redefined, and new species definitions ...the genome to define species has been applied within the genus ...the core/pan-genome ratio can uncover ...
9
Pan-genome Analysis, Visualization and Exploration
... panX analysis pipe- line I have ...from core genome ...phylogenetic analysis of gene clusters and the reconstitution of core genome SNP ...
102
panX: pan-genome analysis and exploration
... isolates––the pan-genome––is often many times larger than the genome of individual ...the core-genome ...Custom pan-genomes can be visualized either using a web server or by ...
12
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 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
... species pan-genome is well- established in comparative prokaryote genomics, it has only recently been extended to comparative intraspecific studies of ...eukaryotic pan-genome analysis ...
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) ...
28
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 ...
20
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 ...
21
Evolution of the core and pan genome of Streptococcus: positive selection, recombination, and genome composition
... of core-genome components because the relative proportion of conspecific donor pieces of DNA is likely to be ...the core- genome was particularly evident in the analysis of the differ- ...
17
The cancer genome atlas pan-cancer analysis project.pdf
... Box 1 tcGa: mission anD strateGy Important information about the biological relevance of the molecular changes in cancer can be obtained through combined analysis of multiple different types of data. For that ...
8
Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
... of core genes by up to one-third for some pipelines ...Draft genome assemblies based on 454 or IonTorrent sequencing include elevated numbers of single-base insertions and deletions due to inaccurate ...
37
Staphylococcus epidermidis pan genome sequence analysis reveals diversity of skin commensal and hospital infection associated isolates
... few genome sequences existed and the most frequent hospital-associated lineage, ST2, had not been fully ...open pan-genome with 80% core genes and 20% variable ...variable genome was ...
13
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract
... The core set from these six genomes contained 1364 ortholo- gous gene clusters as determined by OrthoMCL ana- lysis [39] and 1210 gene clusters, comprising 1652 “unique” genes that occurred at least once in ...
18
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
Clustering of pan- and core-genome of lactobacillus provides novel evolutionary insights for differentiation
... The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20’800 ...Lactobacillus pan- and core-genome resulted in two highly similar ...the ...
17
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
Computational analysis of core promoters in the Drosophila genome
... Drosophila Genome Project informatics group, especially Chris Mungall and ShengQiang Shu for help with the Sim4 align- ments and gene sets, the FlyBase curators for sneak peeks at the chromo- somes as they were ...
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