Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:
- Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
- Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3′ end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5′ ends in the Ecogene data set are located correctly).
- Specificity: Prodigal’s false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
- GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5’+3′) to the Pseudomonas aeruginosa curated annotations.
- Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
- Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
- Open Source: Prodigal source code is freely available under the General Public License.