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.

Cite this paper

Related papers

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs1997
2. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice1994
3. STAR: ultrafast universal RNA-seq aligner2012
4. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability2013
5. MUSCLE: multiple sequence alignment with high accuracy and high throughput2004