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
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
This table contains the following information (only selected columns are explained): Title of column Description Download CLG CLG is a data file with a special
The following data were processed by ChunLab’s 16S Microbiome Profiling Service with EzBioCloud database. You can access the taxonomic profiles without login. Sample NGS
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,
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
A pan-genome is a union of the protein-coding genes (=CDS) in a given set of genomes. Generally, building a pan-genome starts from a set of annotated
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
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.
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
Pan-genome orthologous group (POG) refers to “a group of orthologous genes (orthologs)” that are identified from multiple genomes. The below figure illustrates how POGs are
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
A reliable database is frequently updated, and most importantly, it is systematically organized by best practices with regards to taxonomic classification of prokaryotic organisms. This
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
Genes within a genome are never fixed, even for a very short period of time. That’s why we encounter new bacterial variants with novel antibiotic
QIIME is the most widely used open-source bioinformatics pipeline for microbiome analysis (http://qiime.org/). In this document, we provide a guide for using EzBioCloud’s 16S database
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
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
Definition of Homology, Orthology and Paralogy Homology is a term used when two genes share a common ancestor. The two genes are considered “homologous” or “not homologous” depending
MOTHUR is a widely used, open-source bioinformatics pipeline for microbiome analysis (https://www.mothur.org/). In this document, we provide a guide for using EzBioCloud’s 16S database with
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
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
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
Below you will find the reference to the underline algorithms used through the EzBioCloud and TrueBac ID family of tools and applications. If you cannot
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