Title

Prodigal: prokaryotic gene recognition and translation initiation site identification

Authors

Doug Hyatt, University of Tennessee - KnoxvilleFollow
Gwo-Liang Chen, University of Tennessee - KnoxvilleFollow
Philip F. LoCascio, University of Tennessee - KnoxvilleFollow
Miriam L. Land, University of Tennessee - KnoxvilleFollow
Frank W. Larimer, University of Tennessee - KnoxvilleFollow
Loren J. Hauser, University of Tennessee - KnoxvilleFollow

Document Type

Article

Publication Date

3-8-2010

Abstract

Abstract

Background

The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals.

Results

With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives.

Conclusion

We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/ webcite. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.

Recommended Citation

BMC Bioinformatics 2010, 11:119 doi:10.1186/1471-2105-11-119