Nucleotide sequence similarity values are widely used for identification and description of novel species among bacterial taxonomists. There are many different algorithms available for calculating
This document describes the gene set included the current version of UBCG phylogenomics pipeline [Learn more]. Gene COG category COG ID HMM profile Function alaS
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
Below you will find the reference to the underline algorithms used through the EzBioCloud and TrueBac ID family of tools and applications. If you cannot
For the purposes of all necessary bioinformatics calculations, a complete 16S rRNA gene sequence is defined as the DNA sequence region between universal PCR primers 27F and
What is the UBCG? UBCG stands for the up-to-date bacterial core gene. It is a method and software tool for inferring phylogenetic relationships using a
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
We will work through with an example file. Please download “Leuconostoc_16s.ezb” here and open it with EzEditor2. This file contains 16S sequences of the type
Bacterial infection may be caused by either new species or novel genetic variants in known bacteria that cannot be identified by conventional methods. 16S rRNA (16S)
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
This article will explain how to carry out phylogenetic analysis using EzEditor2 and other programs. We assume that you already aligned all sequences (either 16S
Alignment of two whole genome sequences can be very useful in comparative genomics and it is particularly helpful when alignments are visualized. By this type
Overall genome relatedness index (OGRI) is a term first coined by Chun & Rainey (2014) and represents any measurements indicating how similar two genome sequences
This document explains how to use EzBioCloud’s “Identity” service using single Sanger sequencing data. Preparations Use ab1 file but not a text file. An ab1
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
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
This tutorial will explain how to process a 16S sequence into a phylogenetic tree with EzBioCloud and EzEditor2. 1. Open www.ezbiocloud.net and go to the “Identify”
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
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
Contents What is EzEditor2? EzEditor2 is a nucleotide and amino acid sequence editor that can be used along with EzBioCloud’s Identify and comparative genomics service.
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
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
Overview 16S rRNA stands for 16S ribosomal ribonucleic acid (rRNA), where S (Svedberg) is a unit of measurement (sedimentation rate). This rRNA is an important
Installation of EzEditor2 and related programs EzEditor2 is a JAVA program and requires other external programs to run together. Install the followings before running EzEditor2 program.
ChunLab, Inc
ChunLab Tower, 34 Samseong-ro 85-gil Gangnam-gu Seoul Republic of Korea (ZIP 06194)
EzBiome, Inc
704 Quince Orchard Road, Suite 250, Gaithersburg, Maryland, 20878, United States of America
