Prodigal protocols

Prodigal specifications

Information


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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Documentation


Maintainer


  • person_outline Doug Hyatt <>

Additional information


https://github.com/hyattpd/prodigal/wiki/introduction

Publications for PROkaryotic DYnamic programming Gene-finding ALgorithm

Prodigal IN pipelines

 (19)
2018
PMCID: 5804319
PMID: 29423345
DOI: 10.7717/peerj.4320

[…] the read recruitment results following the workflow outlined by eren et al. (2015). briefly, we first used the program ‘anvi-gen-contigs-database’ to profile prochlorococcus genomes, during which prodigal v2.6.3 (hyatt et al., 2010) with default settings identified open reading frames. we used interproscan v5.17-56 (zdobnov & apweiler, 2001) and eggnog-mapper v0.12.6 (huerta-cepas et al., […]

2017
PMCID: 5334579
PMID: 28254972
DOI: 10.1128/genomeA.01670-16

[…] contig numbers between 24 and 46 per genome with a total size ranging from 2.37 mbp to 2.50 mbp. the g+c content ranged from 53.4% to 53.6%. the protein-coding gene prediction performed using prodigal (v2.60) (5) showed a range of 2,213 to 2,413 sequences per genome. the trnas and rrnas were predicted using aragorn (v1.2.34) (6) and rnammer (v1.2) (7), respectively. the number of trna […]

2017
PMCID: 5374242
PMID: 28360168
DOI: 10.1128/genomeA.00101-17

[…] a total of 4,096,640 paired-end reads., the obtained illumina reads were assembled using the spades software (http://bioinf.spbau.ru/spades) (5). open reading frames (orfs) were predicted using prodigal (6). the predicted bacterial protein sequences were searched using blastp against the clusters of orthologous groups (cog) and the genbank databases. trna gene detection was performed using […]

2017
PMCID: 5544203
PMID: 28777807
DOI: 10.1371/journal.pone.0182484

[…] from ncbi’s protein clusters database (1976 sequences of different proteins involved in dna replication and repair). the orfs of the selected contigs were subsequently predicted using the program prodigal version 2.6.1 [90]. sequences were aligned and phylogenetic trees were constructed with clustalx version 2.1 [91] and further visualised with treeviewx version 0.5.0 [92]., the nucleotide […]

2017
PMCID: 5629052
PMID: 28982995
DOI: 10.1128/genomeA.01029-17

[…] (quality value >20) using trimmomatic version 0.35 (5). the filtered high-quality reads of the sample were assembled into scaffolds using clc genomics workbench, and genes were predicted using prodigal version 2.6.3 with default parameters (6). taxonomic analysis of the predicted genes was carried out using kaiju (7), a program for sensitive taxonomic classification of high-throughput […]

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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