16S rRNA microbiome protocol for Illumina iSeq 100
Technical document from CJ Bioscience, Inc. Title: Experimental protocol for 16S rRNA gene-based microbiome sequencing using Illumina iSeq 100 Sequencing System Document version: 1.0 Background
Tag: Documentation
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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
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
Bacterial Nomenclature 101 and How to Describe a New Species
A short survival guide for microbiologists How are names controlled? Bacterial nomenclature and naming are regulated by the International Code of Nomenclature of Prokaryotes (shortly the
Type strain and reference strain
There is significant confusion between bacterial type strains and reference strains. The type strain is defined in the context of formal bacterial taxonomy whereas reference
[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
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
[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
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.
Bacterial species concept explained
What is a species? A species is often defined as a group of individuals that can actually or potentially interbreed in nature. In practice, this
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
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
Genome annotation
The analysis of all bacterial genome starts with genome annotation. This process can be divided into two steps: Gene-finding step and Functional Annotation step. “Gene-finding”
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
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
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.
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
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
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
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
