True taxonomic identities of ATCC Microbiome Standards
Microbiome standards are important both for the evaluation and effective standardization of methodologies used in microbiome sequencing and bioinformatics analysis. In this document, the genomes
Category: Microbial Isolate Identification
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TrueBac ID – How to upload your genome
TrueBacTM ID upload center currently supports two types of sequence files, namely, FASTA, and FASTQ file(s) (single and paired-end). All these files can be uploaded
Genome-based Identification for Improving Reference Databases
Misidentified or incompletely identified bacterial genome sequences appear frequently in public reference databases. These databases can be significantly improved by genome-based identification against an up-to-date, systematically curated
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
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
[UBCG] programPath file
“programPath” file is a simple text file containing paths of the required external program. For example, all external programs are included in the PATH, it
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)
[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] How to identify bacteria using a single Sanger sequence
This document explains how to use EzBioCloud’s “Identity” service using single Sanger sequencing data. Preparations Use ab1 file but not a text file. An ab1
[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
Starting EzBioCloud with new whole genome data
Welcome to EzBioCloud’s Whole Genome (WG) Analysis service. We assume that you have a new WG data in EzBioCloud cloud system either from genome assembly
[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
[Tutorial] Identifying a bacterial strain using a genome sequence
Welcome! The purpose of this tutorial is to get familiar with EzBioCloud’s many functions, and to be able to apply that knowledge to a scenario
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.
[EzEditor2] 16S “Identify” Workflow with EzBioCloud.net
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”
[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
[EzEditor2] Tutorial
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.
[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
[EzEditor2] Installation
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.
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
