Species Core Genome (SCG)
Definition The Species Core Genome (SCG) is the artificially generated genome sequence that contains the set of core genes within a species. How to construct
Category: EzBioCloud Comparative Genomics
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[Tutorial] Comparison of respiratory tract microbiomes between healthy and diseased humans
Welcome! In this tutorial, we will work with you to compare human respiratory samples between diseased and healthy subjects to get you familiarized with EzBioCloud’s microbiome taxonomic
[OAU] Mac OSX
Step-by-step guide for Apple Mac OSX users First, download necessary files OAU.jar file from here. USEARCH 32bit version for OSX from here. Example file from
[OAU] Manual
Contents About Installation Options Single ANI calculation example Multiple ANI calculation example Contact About OAU is a command line tool for calculating OrthoANI values using
Pan-genome curve
The Pan/Core-genome curves are calculated from Pan-genome Orthologous Groups (POGs) in the data sets. For generating “Pan-genome”, please visit here. For Pan-genome Orthologous Groups, please visit
Pan-genome orthologous group table
This table contains information about pan-genome orthologous groups (POGs) in a data set. For generating “pan-genome”, please visit here. For pan-genome orthologous groups, please visit here.
Pan-genome vs. core-genome
Pan-genome and core-genome can be obtained from multiple genomes in a data set. Both core- and pan-genomes are collections of orthologs or orthologous groups, and
Pairwise Ortholog Matrix
The pairwise ortholog matrix (POM) table was generated by a complete calculation of pairwise ortholog detection in a given dataset. If there are 10 genomes
Genomes in this data set
This table contains the following information (only selected columns are explained): Title of column Description Download CLG CLG is a data file with a special
Pan-genome analysis
A pan-genome is a union of the protein-coding genes (=CDS) in a given set of genomes. Generally, building a pan-genome starts from a set of annotated
Pan-genome orthologous group (POG)
Pan-genome orthologous group (POG) refers to “a group of orthologous genes (orthologs)” that are identified from multiple genomes. The below figure illustrates how POGs are
Gene presence/absence analysis
Genes within a genome are never fixed, even for a very short period of time. That’s why we encounter new bacterial variants with novel antibiotic
Ortholog and its detection
Definition of Homology, Orthology and Paralogy Homology is a term used when two genes share a common ancestor. The two genes are considered “homologous” or “not homologous” depending
[Tutorial] Comparative Genomics of Vibrio cholerae
Welcome! This tutorial was prepared using a well-known pathogenic species, Vibrio cholerae, (the causal agent of cholera). It is a step-by-step example showing how to
Statistical comparison of genomic properties
In this analysis, the following genomic properties are compared to elucidate possible correlation between them. Genome size in Mbp (million base pairs) DNA GC content in
Tetra-Nucleotide Analysis (TNA)
A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides
Overall genome relatedness index (OGRI)
Overall genome relatedness index (OGRI) is a term first coined by Chun & Rainey (2014) and represents any measurements indicating how similar two genome sequences
Gene frequency plot in pan-genome
All potential orthologous protein-coding genes (=CDSs) are clustered into non-redundant gene sets after pan-genome calculation to generate “Pan-genome Orthologous Groups (POGs)”. Obviously, a core part
OrthoANI genomic similarity
OrthoANI (Orthologous Average Nucleotide Identity) is a kind of similarity values between two genome sequences. It is an improved version of the original ANI (Average
