Prodigal specifications


Unique identifier OMICS_01493
Name Prodigal
Alternative name PROkaryotic DYnamic programming Gene-finding ALgorithm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.6.3
Stability Stable
Maintained Yes



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  • person_outline Doug Hyatt <>

Additional information

Prodigal articles

Prodigal citations

PMCID: 5408107

[…] with an n50 length of 223,109 bp. the scaffold with the smallest size was 527 bp, and the scaffold with the biggest size was 827,323 bp., genes were predicted from the assembled scaffolds using the prodigal software, with default parameters (5). a total of 4,766 genes were predicted. the average gene length was 1,006 bp. the length of the smallest gene was 75 bp and the maximum gene length […]

PMCID: 3991649

[…] was obtained using a miseq sequencer (illumina), the mira assembler [28] and clc genomics workbench version 4.9 (clc bio aarhus, denmark). gene predictions were performed using genemarks [29] and prodigal [30] software with default parameters. the genome was annotated manually based on protein homology using blastp searches (basic local alignment search tool) against the non-redundant protein […]

PMCID: 3982105

[…] rrna genes using blastn with a bit score cutoff of >100., transcript profiles from each sample were determined by first subjecting trimmed unassembled reads from each sample to orf calling using prodigal (hyatt et al., 2010). resulting orfs were compared to a translated in-house hydrocarbon gene database using blastp. this database was constructed using all kegg genes involved in hydrocarbon […]

PMCID: 3430607

[…] manufacturer’s suggested default parameters established for 454 datasets. reannotation of the nies 843 reference genome and annotation of the environmental microcystis genes was performed using prodigal [33]., metagenome reads were subjected to a blastx comparison against the ncbi nonredundant database. community taxonomy and function were analyzed in the megan v.4.61.6 analysis toolset […]

Prodigal institution(s)
Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Genome Science and Technology Graduate School, The University of Tennessee, Knoxville, TN, USA; DOE Joint Genome Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
Prodigal funding source(s)
Supported by the U.S. Department of Energy, Office of Science and Biological and Environmental Research Programs.

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