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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




No version available



  • person_outline Doug Hyatt

Additional information

Publications for PROkaryotic DYnamic programming Gene-finding ALgorithm

Prodigal citations


Microbiome Dynamics in a Large Artificial Seawater Aquarium

Appl Environ Microbiol
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] ntamination by using CheckM (). Binning results are presented in Table S5, and bin read recruitment percentages for each sample are presented in Table S6. Open reading frames were identified by using Prodigal () and annotated by using Prokka (). MAG contigs were also queried against the NCBI nr database by using BLASTX. Prokka annotations were queried for genes involved in aerobic and anaerobic re […]


Complete Genome Sequence of Multiple Antibiotic Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus)

Genome Announc
PMCID: 5920164
PMID: 29700142
DOI: 10.1128/genomeA.00248-18
call_split See protocol

[…] gapless contigs (2,128,740 bp and 23,538 bp) were obtained after sequence assembly. Gene prediction was conducted using tRNAscan-SE () for tRNA search, Rfam () for rRNA and noncoding RNA search, and Prodigal () for coding sequence (CDS) search. Predicted genes were functionally annotated by homology search against Kyoto Encyclopedia of Genes and Genomes (KEGG) (), SEED (), Swiss-Prot (), and eggN […]


Draft Genome Sequence of the Extremely Desiccation Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1

Genome Announc
PMCID: 5920166
PMID: 29700137
DOI: 10.1128/genomeA.00216-18

[…] processed with the SqueezeM pipeline (J. Tamames, unpublished data). Briefly, they were assembled using MEGAHIT v1.1.2 (), and open reading frames (ORFs) and rRNA coding sequences were predicted with Prodigal v2.6.2 () and barrnap v0.9-dev (, respectively. ORFs were aligned against the Kyoto Encyclopedia of Genes and Genomes (KEGG) () and Clusters of Orthologous […]


Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution

PLoS One
PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] Contiguator [] and ACT 10.2.0 []. The Illumina reads were remapped to the scaffolds using Bowtie 0.12.7[] and visualized by Tablet[]. Annotation was primarily done by Prokka[], which uses Prodigal 2.6 [] to predict gene sequence similarity analysis. GO annotations were assigned by Blast2GO[]. Mauve was applied for whole chromosome genome comparison and plasmid genome comparison []. A c […]


Genome Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate Oxidising Bacteria

PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] Automated gene modelling was performed using the Microbial Genome Annotation & Analysis Platform MaGe [], a bacterial genome annotation system. Genes were identified using Prodigal [] and AMIGene [] as part of the MaGe genome annotation pipeline. The predicted CDSs (coding sequences) were translated and were used to search the National Center for Biotechnology Informati […]


Genome centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Biotechnol Biofuels
PMCID: 5911951
PMID: 29713376
DOI: 10.1186/s13068-018-1121-0

[…] (Additional file ) were co-assembled using IDBA-UD [] with a maximum k-mer size of 100 and a minimum contig length of 800 bp. Open Reading Frames (ORFs) of the assembled contigs were predicted using Prodigal v2.60 [] in metagenome mode. Putative protein functions were obtained by mapping ORFs to the SEED (release 70) [], COG (2003-205) [] and NCBI non-redundant (retrieved 26 July 2016) databases […]


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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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