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
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
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
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
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
[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
[Tutorial] Comparative Genomics of Vibrio cholerae
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
Microbiome Taxonomic Profile (MTP) Documentation & Glossary
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
How to calculate 16S rRNA sequence similarity values for bacterial taxonomy: Why BLAST should be avoided
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
[UBCG] Gene set
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
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
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
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] 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)
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
[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
