AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run with pre-trained parameters on this web server or be downloaded and run locally. It is open source so you can compile it for your computing platform. You can also run AUGUSTUS on the German MediGRID. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users.

The AUGUSTUS training web server application automatically generates training gene sets from genomic sequence(s) and a set of Proteins or ESTs and subsequently trains AUGUSTUS parameters for a new species, and runs gene predictions with the new parameters and the supplied extrinsic evidence. Alternatively, you can also download the autoAug.pl pipeline and execute our training and prediction pipeline locally.


Features


Gene prediction with AUGUSTUS


Training AUGUSTUS


Parameters are already available for the following species:

AUGUSTUS has currently been trained on species specific training sets to predict genes in the following species. Note that for closely related species usually only one version is necessary. For example, the human version is good for all mammals. Contributions.
animals:                 alveolata:                 plants and algae:            fungi:
Acyrthosiphon pisum
Aedes aegypti
Amphimedon queenslandica
Apis mellifera
Brugia malayi
Caenorhabditis elegans
Callorhinchus milii
Culex pipiens
Drosophila melagonaster
Homo sapiens
Nasonia vitripennis
Petromyzon marinus
Schistosoma mansoni
Tribolium castaneum
Tetrahymena thermophila
Toxoplasma gondii
Arabidopsis thaliana
Chlamydomonas reinhardtii
Galdieria sulphuraria
(Nicotiana tabacum)
Solanum lycopersicum
Zea mays
Aspergillus fumigatus
Aspergillus nidulans
Aspergillus oryzae
Aspergillus terreus
Botrytis cinerea
Candida albicans
Candida guilliermondii
Candida tropicalis
Chaetomium globosum
Coccidioides immitis
Coprinus cinereus
Cryptococcus neoformans
Debaryomyces hansenii
Encephalitozoon cuniculi
Eremothecium gossypii
Fusarium graminearum
Histoplasma capsulatum
Kluyveromyces lactis
Laccaria bicolor
Lodderomyces elongisporus
Magnaporthe grisea
Neurospora crassa
Phanerochaete chrysosporium
Pichia stipitis
Rhizopus oryzae
Pneumocystis jirovecii
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Ustilago maydis
Verticillium longisporum
Yarrowia lipolytica

Examples of AUGUSTUS predictions can be viewed at at various genome browsers:

UCSC Genome Browser, Wormbase: Caenorhabditis elegans, C. briggsae, C. remanei, Brugia malayi
Phytozome: Chlamydomonas reinhardtii
Flybase: Drosphila melanogaster
Genboree Browser: Tribolium castaneum