Faculty Publications and Other Works -- Division of Biology

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.

Files over 3MB may be slow to open. For best results, right-click and select "save as..."

Included in

Biology Commons

Share

COinS