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EasyGene 1.2b Server

Gene finding in prokaryotes

The EasyGene 1.2 server produces a list of predicted genes given a sequence of prokaryotic DNA. The current version contains models for 138 different organisms. Each prediction is attributed with a significance score (R-value) indicating how likely it is to be just a non-coding open reading frame rather than a real gene. All that is required of you as a user is to supply the query sequence(s) and to select the organism model to use (see instructions).

The pre-calculated EasyGene 1.2 predictions for the complete genomes of the 138 organisms can be downloaded from the EasyGene site at BINF at the University of Copenhagen.

This version replaces EasyGene 1.0. View the version history of this server.

Instructions Output format Article abstracts


Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

Organism               View the organism list.

R-value cutoff                 Predict suboptimal gene starts

At most 10,000,000 nucleotides per submission in at most 50 sequences.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

Large-scale prokaryotic gene prediction and comparison to genome annotation.
P. Nielsen and A. Krogh.
Bioinformatics: 21:4322-4329, 2005.

PMID: 16249266         View the abstract

EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance.
Thomas Schou Larsen and Anders Krogh.
BMC Bioinformatics: 4:21, 2003

PMID: 12783628         View the abstract         View the full article


Would you like to gene train own models for other organisms than the 138 mentioned above? The EasyGene 1.2 training part is available as a stand-alone software package (for Linux only). There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: