Prodigal: prokaryotic gene recognition and translation initiation site identification
- ORNL
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. 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. 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. The goals of Prodigal were to attain greater sensitivity in identifying existing genes, to predict translation initiation sites more accurately, and to minimize the number of false positive predictions. The results of Prodigal were compared to existing methods for both purely experimentally verified genes as well as curated Genbank files for a number of genomes. Prodigal's performance was found to be comparable or better to existing methods in the prediction of genes while also predicting fewer overall genes. In the prediction of translation initiation sites, Prodigal performed competitively with existing methods. Prodigal is currently already in use at many institutions, and it has been used to annotate all finished microbial genomes submitted to Genbank by DOE-JGI in 2008 and onward (a substantial percentage of the overall finished microbial genomes at NCBI). It is run regularly at NCBI alongside GenemarkHMM and Glimmer, and it has also been incorporated into the Swiss Institute of Bioinformatics microbial genomics browser. In conclusion, Prodigal should prove to be a valuable resource for genome annotation of either draft or finished microbial sequence.
- Research Organization:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- DE-AC05-00OR22725
- OSTI ID:
- 1045318
- Journal Information:
- BMC Bioinformatics, Vol. 11
- Country of Publication:
- United States
- Language:
- English
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