Learn to use CMR, the Comprehensive Microbial Resource, for the analysis of prokaryote genomes. CMR includes the complete sequences of all publicly available microbial genomes with available tools for cross-genome analysis. Data is seamlessly integrated to allow users to explore information from the level of the gene, to the genome, to the comparative analysis of multiple species. A convenient and easy-to-use suite of tools allow you to rapidly design, view, and interpret huge data sets with fun graphs and visualizations. Containing over 400 genomes (and more than a gigabase of DNA sequence), CMR is a treasure-trove of microbial genome information.

Notice: An undated note on the CMR page reads "CMR is no longer supported and has been taken offline. If you are interested in supporting this project or a collaboration, please contact Lauren Brinkac". We have attempted to determine if mirrors or a new instance will be made available and keep you posted.

You will learn:

  • how to query for genes and genomes from CMR
  • to analyze a gene, from its sequence level to its biological function
  • to explore genomes from different perspectives
  • how to use a vast array of visualization tools to compare genomes from multiple organisms
  • to save genes and genomes into your own tool Cart for in-depth analysis


This tutorial is a part of the tutorial group Microbe resources. You might find the other tutorials in the group interesting:

Complete Microbial Genomes: An extensive collection of data, resources and tools for prokaryotic genomic analysis

Viral Genomes at NCBI: Viral genome resources including single-stranded or double-stranded RNA or DNA viruses

Integrated Microbial Genomes (IMG): IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.

Integrated Microbial Genomes with Microbiome samples (IMG/M): IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence

VBRC: The Viral Bioinformatics Resource Center

UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.

GenoCAD Advanced Topics: Computer-Assisted Design software for synthetic biology

GenoCAD: Computer-Assisted Design software for synthetic biology


Genome Databases (prok + viral) : Genomic databases or repositories primarily aimed at prokaryotic or viral organisms. Some may contain eukaryotic data as well.

Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.


Tip of the Week: Whole Cell Simulation software: My twitter feed exploded over the last few days with conflama around the new publication about the simulation of the biological processes in a cell. Most of the ire was aimed at a fawning NYT piece tha...


Recent BioMed Central research articles citing this resource

Sun Tao et al., A novel small RNA CoaR regulates coenzyme A biosynthesis and tolerance of Synechocystis sp. PCC6803 to 1-butanol possibly via promoter-directed transcriptional silencing. Biotechnology for Biofuels (2017) doi:10.1186/s13068-017-0727-y

Wen Zhiyun et al., Recombinant expression of Chlamydia trachomatis major outer membrane protein in E. Coli outer membrane as a substrate for vaccine research Clinical microbiology and vaccines. BMC Microbiology (2016) doi:10.1186/s12866-016-0787-3

Feng Sai-Xiang et al., Ralstonia solanacearum fatty acid composition is determined by interaction of two 3-ketoacyl-acyl carrier protein reductases encoded on separate replicons. BMC Microbiology (2015) doi:10.1186/s12866-015-0554-x

Kohler Christian et al., A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium Microbial genetics, genomics and proteomics. BMC Microbiology (2015) doi:10.1186/s12866-015-0404-x

Chin Chui-Yoke et al., Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence Prokaryote microbial genomics. BMC Genomics (2015) doi:10.1186/s12864-015-1692-0