V. cholerae 2016 outbreak

About This Data Set

Set name

No. of genomes

Comment from CJ Bioscience

This data set has 22 genomes.

Statistical Comparison of Genomic Properties

Phylogenomics by OrthoANI analysis

OrthoANI is a relatedness measure (as %) between two genomes. Newick tree files can be opened by MEGA program and CSV files by Spreadsheet programs such as MS Excel.

Phylogenomics By Tetra-nucleotide Analysis

Tetra-nucleotide analysis is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Newick tree files can be opened by MEGA program and CSV files by Spreadsheet programs such as MS Excel.

Pairwise Ortholog Matrix

Reference Genome:

≥ 99% ≥ 95% ≥ 90% < 90% Non-reciprocal No Hit

Genome Alignment by NUCMER program

NUCMER is a popular whole genome alignment tool developed by Delcher et al. (2002) The graphical output of NUCMER can be used to detect genomic inversion and many other differences between two genomes.
Click here to learn more about NUCMER.

Frequency Plot of Pan-genome Orthologous Group(POGs)

Frequency Plot of POGs(with Major COG Categories)

Functional Categories by COG/EggNog Scheme

Functional Categories by SEED Scheme

Pan-genome Orthologous Groups (POGs)

Venn Diagram

Please select Genome at least of 2 from the list.

Pan-genome Orthologous Groups (POGs)

Strain-specific CDSs

Core size: POGs (Defined by 95%)

*POGs = Pan-genome Orthologous Groups

Identify Differentially Present Pan-genome Orthologous Groups(POGs) and KEGG Pathways

Gene Presence/Absence (Gene Content) Analysis

Gene presence/absence matrix of all CDSs

Gene presence/absence matrix of differential CDSs

Pan/Core-genome curve

BLAST Search

All Data Set	From Publication	Human Gut	Human Pathogen
Model Organisms	Plant Pathogen	Probiotics	Archaea
Animal Pathogen	Fish Pathogen	Food Poison	Biothreat
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