Frequently Asked Questions

Introduction into IMG video on YouTube:  JGI's Integrated Microbial Genomes and Metagenomes (IMG) system

View our Webinar Series on  YouTube.

For more information and Q & A see IMG Webinar.

Topics that were covered:

• IMG Sequence Similarity Search (Blast)

• Analysis Carts and Workspace

• Statistical Analysis Tool

• ANI (Average Nucleotide Identity)

• Genome Search - Advanced Search Builder

• IMG data export and download

• Metagenome Bins

• Data Submission & Management

Using IMG is free to use. You do not need an account to use public IMG/M. But public IMG has limited features and tools.
IMG/MER which requires an JGI SSO account has many more features: Workspace, new Statistical Analysis Tools, and more.

You can sign up for an account at: JGI Single Sign On (JGI SSO)

Login Issues

• I'm stuck on the log in page.

Logout at JGI SSO https://signon.jgi.doe.gov/ and clear all browser's cookies and cache

• I created an account, but IMG said I already have an account. Please contact us.

See our glossary of terms used in IMG and GOLD.

• We use Google Services; analytics and reCAPTCHA etc...

• Some ISP's DNS servers are blocking signon.jgi.doe.gov. Try using openDNS or Google's DNS servers.

• You must allow 3rd party cookies and accept both https and http content.

• Please see full system requirements here

• Data Sources

• Plasmids

• Eukaryotic Genomes in IMG

• Object Identifiers

• Function Database Versions

• Lineage

• Architecture

• Data Model

• Data Processing

• Data Analysis

Q: Is the IMG available for local installations so that we could incorporate our own microbial genome data into IMG on our own servers?
A: IMG is not available for local installations. Resources required for making the IMG collection of tools and databases ready for installation at other sites are not available at this time.

Q: How is IMG different from other systems like PUMA, or SEED?
A: While IMG shares goals with systems such as PUMA and SEED (see IMG Lineage), IMG's main goal is to support the analysis of the genomes sequenced at JGI.

Q: What is "Finished", "Draft", "Permanent Draft" and so on?
A: Draft: It's incomplete and therefore a draft. More complete versions of genomes are likely to appear.
Finished: It's complete. There won't be new versions unless errors are found.
Permanent Draft: It's still incomplete, but it's pretty good already. There is no plan to further improve the version

See section Carts and Workspace 

See section Carts and Workspace 

IMG download requires an JGI SSO account.

See IMG Webinar series "IMG data export and download" on how to download IMG data sets.

Other download documentation, please see IMG Help section Download.

Please see section Submission FAQ 

How does Gene Detail page Conserved Neighborhood "Show neighborhood regions with the same top COG hit (via top homolog)" work?

The hits are from isolate blast all (top 500 hits) with the following filters:

• All gene hits must have a COG annotation.

• All self hits were removed.

• Show only genome cart hits if it is not empty.

• Remove any hits with a bit score > 10000.

• Remove any hits with a percent identity < 50%.

• Length filterung:

  • Remove hits with length > max length ( where max length = query sequence length * 1.3 )

  • Remove hits with length < min length ( where min length =  query sequence length * 0.7 )

See  Alternative to Gene Conserved Neighborhood to get Gene Neighborhoods without filtering,

The following IMG Data Portals have been deprecated or replaced.

• IMG/HMP website has been deprecated. All the HMP's data sets are still available in IMG/M.

• IMG/ABC website has been replaced. Please see Secondary Metabolism Collaboratory SMC.