[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
American Type Culture Collection (ATCC) commercially provides several standard products for microbiome sequencing. Often their taxonomic label is not correct due to the technical limitation
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.
16S rRNA microbiome protocol for Illumina iSeq 100
Technical document from ChunLab, Inc. Title: Experimental protocol for 16S rRNA gene-based microbiome sequencing using Illumina iSeq 100 Sequencing System Document version: 1.0 Background The
EzBioCloud 16S database
Publications that introduced the EzBioCloud 16S database Our database has been introduced in the following three publications (The numbers of citations are as of Mar.
Starting EzBioCloud with new whole genome data
Welcome to EzBioCloud’s Whole Genome (WG) Analysis service. We assume that you have a new WG data in EzBioCloud cloud system either from genome assembly
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
[Resource] 16S rRNA gene sequences of the human gut microbiota
This page contains example 16S rRNA sequences of the human gut microbiota. Data was generated by the conventional Sanger capillary sequencing method and published by
Firmicutes to Bacteroidetes Ratio
Firmicutes and Bacteroidetes are two major phyla of the domain Bacteria and dominant in human gut microbiota. The Firmicutes to Bacteroidetes ratio (F/B ratio) has been extensively
[Tutorial] Identifying a bacterial strain using a genome sequence
Welcome! The purpose of this tutorial is to get familiar with EzBioCloud’s many functions, and to be able to apply that knowledge to a scenario
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
