[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
Author: CJ Bioscience, Inc.
Subscribe To Our Newsletter
Get updates and learn from the best
Genomospecies
Prokaryotic (bacterial or archaeal) species are now generally defined by genomic methods such as average nucleotide identity (ANI). A genomospecies is a species that can be
[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
How to use EzBioCloud MTP data for external programs
EzBioCloud Microbiome Taxonomic Profile data can be exported as a plain text file for you to use with other software tools such as the R package.
[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
[Tutorial] Exploring kimchi microbiota
Kimchi is a traditional side dish made from salted and fermented vegetables. When the fermentation is right, the pH of the cabbage kimchi reaches ~4.2.
Example files for Microbiome Taxonomic Profile pipeline
The below are the example files for you to test drive Microbiome Taxonomic Profile (MTP) pipeline of the EzBioCloud cloud. Illumina MiSeq paired-end data of a
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
EzBioCloud Genome Database
The EzBioCloud Genome Database is a part of EzBioCloud.net. It is maintained by CJ Bioscience, Inc. to provide best-curated genome database of Bacteria and Archaea.
Complementary comparative genomics set
A Complementary CG (comparative genomics) set is a CG set that is complementarily provided by the EzBioCloud team to the users of the Whole Genome
MTP (Microbiome Taxonomic Profile)
MTP (Microbiome Taxonomic Profile) is a unit of data that contains the taxonomic profile of a sample. At present, we provide MTP for bacterial and
[Tutorial] How to browse individual Human Microbiome Project (HMP) data
Human Microbiome Project funded by US National Institutes of Health (NIH) resulted in the taxonomic profiling data of microbiomes on 19 body sites of 242
zZ-format
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
[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.
Taxonomic group
“Taxonomic group” in EzBioCloud 16S database Even though 16S rRNA gene has been widely used in the classification and identification of Bacteria and Archaea, it has
Plasmid and megaplasmid
A plasmid is a DNA molecule that is not chromosomal or extra-chromosomal. It is found in Bacteria and Archaea, and not essential to survival. A
[Tutorial] Comparison of respiratory tract microbiomes between healthy and diseased humans
Welcome! In this tutorial, we will work with you to compare human respiratory samples between diseased and healthy subjects to get you familiarized with EzBioCloud’s microbiome taxonomic
