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
Comparison between V3V4 and full-length sequencing of 16S rRNA genes
Microbiome taxonomic profiling (MTP) is a method to elucidate taxonomic composition of the complex microbial community. The currently available and widely used NGS platforms are
Taxonomic profile of human microbiome at EzBioCloud.net
Taxonomic profile of human microbiome at EzBioCloud.net EzBioCloud 16S database provides a comprehensive taxonomic backbone of Bacteria. Here we applied the sophisticated bioinformatics pipeline for
TrueBac ID – How to upload your genome
TrueBacTM ID upload center currently supports two types of sequence files, namely, FASTA, and FASTQ file(s) (single and paired-end). All these files can be uploaded
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
Microbiomes revealed by taxonomic profiling
The following data were processed by ChunLab’s 16S Microbiome Profiling Service with EzBioCloud database. You can access the taxonomic profiles without login. Sample NGS
[Tutorial] Discover Biomarkers Facilitating Anti-PD-L1 Efficacy
Discover Biomarkers Facilitating Anti-PD-L1 Efficacy The gut microbiota plays an important role in shaping systemic immune responses. In a study published in the journal Science,
Genome-based Identification for Improving Reference Databases
Misidentified or incompletely identified bacterial genome sequences appear frequently in public reference databases. These databases can be significantly improved by genome-based identification against an up-to-date, systematically curated
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
Example files for Microbiome Taxonomic Profile pipeline
The below are the example files for you to test drive Microbiome Taxonomic Profile (MTP) pipeline of the EzBioCloud cloud. Illumina MiSeq paired-end data of a
