Completeness of 16S rRNA gene sequence
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
[UBCG] User’s manual
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
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
[EzEditor2] Working with 16S rRNA sequences
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 identification in clinical diagnostic laboratories using 16S rRNA sequences
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)
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
[EzEditor2] Phylogenetic analysis
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
Whole genome alignment using NUCMER
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)
Overall genome relatedness index (OGRI) is a term first coined by Chun & Rainey (2014) and represents any measurements indicating how similar two genome sequences
[Tutorial] How to identify bacteria using a single Sanger sequence
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
[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
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
[EzEditor2] 16S “Identify” Workflow with EzBioCloud.net
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”
[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
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
[EzEditor2] Tutorial
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.
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
[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
16S rRNA and 16S rRNA Gene
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
[EzEditor2] Installation
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.
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
[Tutorial] Exploring kimchi microbiota
Kimchi is a traditional side dish made from salted and fermented vegetables. When the fermentation is right, the pH of the cabbage kimchi reaches ~4.2.
[UBCG] programPath file
“programPath” file is a simple text file containing paths of the required external program. For example, all external programs are included in the PATH, it
True taxonomic identities of ATCC Microbiome Standards
Microbiome standards are important both for the evaluation and effective standardization of methodologies used in microbiome sequencing and bioinformatics analysis. In this document, the genomes
