Agene automatically generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome. We apply a Hidden Markov model (HMM) that implements explicit length distribution modelling for all gene structure blocks using acyclic discrete phase type distributions. The state structure of the each HMM is generated dynamically from an array of sub-models to include only gene features represented in the training set. Refer to Munch and Krogh (2006) for details on Agene.

Performance of Agene:
Summary statistics for the current performace on each eukaryotic genome can be viewed here.

The Agene software:
Agene is freely available for academic and non-comercial use through our download site. Interest in a commercial use of Agene should be directed to Kasper Munch. Agene is composed by two parts that can be used and downloaded independently:
  • agene-builder:
    This script runs the automatic build of gene structure models based on a set of mRNA and genome.
  • agene-predictor:
    This script runs the prediction on sequence using pre-built models.

Important: This webservice is not intented for prediction of genes on whole chomosomes or genomes. Cached predictions on all fully sequenced genomes can be acessed and browsed through the Agene Prediction Library in the near future.

Upload inputdata for Agene:

You can submit data as a file or text typed in the text-field below. Note that even the smallest job will take about a few minutes to complete.
As of now a maximum size of 10MB is imposed on file and text size.

Data file:

Paste in data sequences:

Select a species:
Both forward and reverse stand:

Email notification (when done):