Prodigal: prokaryotic gene recognition and translation initiation site identification

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/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.

Figure 1

Pseudocode description of the Prodigal algorithm.

Figure 2

Illustration of the dynamic programming connections in Prodigal. The red arrows represent gene connections, and the black arrows represent intergenic connections. (a) 5' forward to 3' forward: Gene on the forward strand. (b) 3' forward to 5' forward: Intergenic space between two forward strand genes. (c) 3' forward to 3' forward: Overlapping genes on the forward strand. (d) 3' forward to 5' reverse: Forward and reverse strand genes whose 3' ends overlap. (e) 5' reverse to 3' reverse: Intergenic space between two reverse strand genes. (f) 3' reverse to 5' reverse: Gene on the reverse strand. (g) 3' reverse to 3' reverse: Overlapping genes on the reverse strand. (h) 5' reverse to 5' forward: Intergenic space between two opposite strand genes. (i) 3' forward to 3' reverse: Intergenic space between two opposite strand genes.