[Quiz] Sequence similarities of small subunit rRNA genes
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
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
This tutorial will explain how to process a 16S sequence into a phylogenetic tree with EzBioCloud and EzEditor2. 1. Open www.ezbiocloud.net and go to the “Identify”
Step-by-step guide for Apple Mac OSX users First, download necessary files OAU.jar file from here. USEARCH 32bit version for OSX from here. Example file from
Contents About Installation Options Single ANI calculation example Multiple ANI calculation example Contact About OAU is a command line tool for calculating OrthoANI values using
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
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
Contents What is EzEditor2? EzEditor2 is a nucleotide and amino acid sequence editor that can be used along with EzBioCloud’s Identify and comparative genomics service.
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
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.
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
On this page we’ve put together an archive of the 2017 EzBioCloud database updates. We aim to maintain our database regularly, with scheduled updates once
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
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
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
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
A pseudogenome is a virtual, artificial concatemer of all assembled contigs from sequencing a particular genome. It is computationally generated after sequencing a genome, and
The genome map is a circular representation of one or several genomes that provides a quick and easy way to spot global patterns, large features,
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
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
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