Agmial is an integrated system for bacterial genome annotation.
It has been developed with the following requirements in mind:
- maximize annotation automation,
- ability to work on draft sequences,
- keep the program modular and extensible,
- choose informatics and bioinformatics standards when possible
(e.g. Web Services, RDBMS, ...)
- distribute the program under an open-source license.
A demonstration version of agmial is available here
The login is agmialRead and the password
A version of agmial with some public genomes re-annoted is available here
- K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin JF. Gibrat. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Research. Jul 2006. [Pubmed]
Eric Duchaud, Mekki Boussaha, Valentin Loux, Jean-François Bernardet, Christian Michel, Brigitte Kerouault, Stanislas Mondot, Pierre Nicolas, Robert Bossy, Christophe Caron, Philippe Bessieres, Jean-François Gibrat, Stéphane Claverol, Fabien Dumetz, Michel Le Hénaff, Abdenour Benmansour. Complete genome sequence of the fish pathogen Flavobacterium psychrophilumNat Biotechnol2007 [Pubmed]
- M. van
de Guchte , S. Penaud , C. Grimaldi , V. Barbe , K. Bryson, P. Nicolas, C. Robert, S. Oztas, S. Mangenot, A. Couloux, V. Loux<, R. Dervyn, R. Bossy, A. Bolotin, JM. Batto, T. Walunas, JF. Gibrat, P. Bessieres, J. Weissenbach, SD. Ehrlich, E. Maguin.The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America. Jun 2006. [Pubmed]
- S. Chaillou, M. Champomier-Verges, M. Cornet, A-M Crutz
Le Coq, A-M.Dudez, V. Martin, S. Beaufils, E. Darbon-Rongere, R. Bossy,
V. Loux and M. Zagorec. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nature Biotechnology December 2005. [Pubmed]
Agmial is used or has been used to annotate :
- Flavobacterium psychrophilum and other flavobacter
(Virologie et Immunologie Moléculaire,INRA Jouy en Josas
Department ) [Public server] [Private server] [Artemis].
- Lactobacillus bulgaricus (Genetique Microbienne,INRA Jouy en Josas , MICA department)[Private server] [Artemis].
- Lactobacillus sakei(Flore Lactique et Environnement Carné ,INRA Jouy en Josas , MICA department) [Public server] [Private server] [Artemis].
- Propionibacterium freudenrichii( Science et technologie du lait et de l'oeuf ,INRA Rennes , MICA department) [Private server] [Artemis].
- Staphylococcus xylosus( Microbiologie MIC,INRA Theix , MICA department) [Private server] [ [Artemis].
- Streptococcus salivarius JIM8777 and JIM8780 (Genetique Microbienne,INRA Jouy en Josas , MICA department)[Private server] [Artemis].
- Arthrobacter arilaitensisand other genomes( GMPA,INRA Grignon , MICA department) [Private server] [ [Artemis].
- And other private genomes ...
Trouble with Artemis? Check Artemis
User Guide and Faq
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.
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
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:
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
Screenshot of the CAM (Contig Analysis Manger) web interface
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:
- integrate new tools (RMES, RHOM, TMHMM,...),
- develop whole genome comparison methods (gene context, genome alignment...)
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
- Philippe Bessières
- Xavier Benigni
- Robert Bossy
- Kevin Bryson
- Cédric Soubrié
- Nicolas Dehais
- Frederic Papazian
- Jean-François Gibrat
- Valentin Loux
- Pierre Nicolas
- Mickael Quentin
- Amal Hammani
- Pascal Bento