Agmial is an integrated system for bacterial genome annotation. It has been developed with the following requirements in mind:


A demonstration version of agmial is available here (artemis).
The login is agmialRead and the password agmialRead

A version of agmial with some public genomes re-annoted is available here (artemis).



Agmial is used or has been used to annotate :

Trouble with Artemis? Check Artemis User Guide and Faq


Jean-François Gibrat ,Valentin Loux.


The Agmial architecture involves two independent modules: the Contig Analysis Module (CAM) and the Protein Analysis Module (PAM). They are respectively responsible for storing and applying bioinformatics tools on DNA and proteins sequences. The system currently integrates 20 different third-party programs including the SHOW gene detector, Blast and the Interpro suite. Thanks to the modular architecture of Agmial, the addition of new tools represents a marginal effort of development.

agmial schema
Agmial schema

In order to synchronize the annotations of proteins on PAM and their corresponding CDS on CAM, modules communicate through the SOAP protocol; as a matter of fact both modules are web service providers. The end-user may interact with the system through either a web browser, either a Web Services client: we currently use a modified version of Artemis.

Usage data flow

The close cooperation between the system and the experts leads to an accurate annotation of the genome. The end-user is usually a team of annotators who works on a specific organism: they input the draft genome sequence, CAM searches for CDSs, passes the translated proteins to PAM which looks for homologies and domains.

After all the processing, the system suggests a functional annotation for each protein, then the annotators validate and refine it. The following diagram represents the information exchanged during the annotation process:

typical scenario
Typical scenario

Each time annotations change, PAM and CAM communicate in order to synchronize their information. The users can directly update features on CAM (with Artemis), update proteins annotations on PAM with the web interface (see screenshot), or update the contig batches as the sequencing evolves. In the latter case, the manual annotations are kept from a batch to another

CAM screenshot
Screenshot of the CAM (Contig Analysis Manger) web interface and artemis.

PAM screenshot
Screenshot of the PAM (Protein Analysis Manger) web interface.


Collaboration with annotators has raised issues about a number of additional required features which are currently in development:


Acces to source code

Agmial is distributed under GPL license.If you want to have access to the source code,please take a few seconds to fill this form and we will give you access to the latest agmial tarball.


Agmial is (or has been) developped by the following people (alphabetically):