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
How to use EzBioCloud MTP data for external programs
EzBioCloud Microbiome Taxonomic Profile data can be exported as a plain text file for you to use with other software tools such as the R package.
Identification of Lachnospiraceae bacterium 5_1_63FAA
The genome sequence that is labeled as “Lachnospiraceae bacterium 5_1_63FAA” has been included in most microbiome taxonomic profiling software tools, and has therefore appeared in
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
Species-level microbiome analysis using EzBioCloud 16S Database
Species-level microbiome analysis using EzBioCloud EzBioCloud 16S database is designed to be best performed for species-level identification even though there is a limitation due to
Check List for 16S-based Microbiome Analysis
A reliable database is frequently updated, and most importantly, it is systematically organized by best practices with regards to taxonomic classification of prokaryotic organisms. This
Identification of Ruminococcus sp. 5_1_39BFAA
Many genome sequences in public databases are used in metagenomic studies to understand the human microbiome. Unfortunately, many of the taxonomic identities of these genomes
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
How to use EzBioCloud 16S database with QIIME
QIIME is the most widely used open-source bioinformatics pipeline for microbiome analysis (http://qiime.org/). In this document, we provide a guide for using EzBioCloud’s 16S database
[Tutorial] How to browse individual Human Microbiome Project (HMP) data
Human Microbiome Project funded by US National Institutes of Health (NIH) resulted in the taxonomic profiling data of microbiomes on 19 body sites of 242
[UBCG] example commands
Run these lines to generate bcg files from fasta files. java -jar UBCG.jar extract -bcg_dir bcg -i fasta/CP012646_s_GCA_001281025.1_KCOM_1350.fasta -label “CP012646_s KCOM 1350” -acc “GCA_001281025.1” -taxon
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
How to use EzBioCloud 16S database with MOTHUR
MOTHUR is a widely used, open-source bioinformatics pipeline for microbiome analysis (https://www.mothur.org/). In this document, we provide a guide for using EzBioCloud’s 16S database with
