[Quiz] Comparative microbiome analysis
How to search the literature and next-generation sequencing(NGS) database How to download NGS data How to analyze taxonomic profiles of microbiome data How to compare
How to search the literature and next-generation sequencing(NGS) database How to download NGS data How to analyze taxonomic profiles of microbiome data How to compare
Install SRA toolkit on your computer To download any file from the NCBI SRA database, you need to install SRA toolkit software from NCBI SRA Toolkit.
Majority of microbiome taxonomic profile data are based on 16S rRNA gene targetting bacteria. In this document, I will explain how to search and locate
This is a collection of articles and resources for prokaryotic taxonomy and microbiome study. This is developed by Jon Jongsik Chun at Seoul National University,
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
Objectives: Understanding the DNA sequence searching algorithm and difference from the sequence similarity calculation. Please do the followings: Select randomly five 16S sequences from this
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,
Several standards products are available to validate 16S microbiome sequencing procedures. They are usually a mixture of genomic DNAs or whole cells from different species
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
In descriptive statistics, a box plot or boxplot is a visualization method for graphically depicting groups of numerical data through their quartiles. Here, we will
Clostridium clusters XIVa and IV are groups of bacteria that have been known as major players in the human microbiome(Hold et al., 2002;Frank et al.,
In this course, you will learn how to identify bacterial isolates using genome sequence. Please read the following materials first. Bacterial species concept Tutorial on
Probiotics are defined as live microorganisms that are thought to provide health benefits when consumed. The most popular probiotic organisms are bacteria belonging to a
Clusters of Orthologous Groups (COGs) are sets of orthologous protein-coding sequences that can be used to rapidly assign functional annotations to whole genome sequences. In
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
Objectives: Small subunit ribosomal RNA (rRNA) gene is one of the most widely used phylogenetic markers or DNA barcodes. A similarity between two DNA sequences is
In this tutorial, we will work you through how to use EzEditor2 for the alignment of protein-coding genes. We will use an example file named
The following color codes are used in EzBioCloud service to indicate major bacterial phyla. The below figure represents bacterial diversity based on 16S rRNA gene
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”
In this class, we will try to identify genomic islands (GI; DNA containing multiple genes that are often transferred between bacterial strains) and track down
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