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
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
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,
What is the zZ-format? zZ format is typically composed by zZ+unique id or accesscion+zZ (e.g. zZCP001758zZ or zZ12494zZ). These zZ-formatted labels are used in plain text
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
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.
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”
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
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
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
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
Overall genome relatedness index (OGRI) is a term first coined by Chun & Rainey (2014) and represents any measurements indicating how similar two genome sequences
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
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