Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory.


  • Reference: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ, Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics11 (1):119 2010 Mar 8.


To see what versions of PRODIGAL are available type

module avail prodigal

To see what other modules are needed, what commands are available and how to get additional help type

module help prodigal

To use PRODIGAL, include a command like this in your batch script or interactive session to load the prodigal module:

module load prodigal

Be sure you also load any other modules needed, as listed by the module help prodigal command.


Command line usage

prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type] [-g tr_table] [-h]
  [-i input_file] [-m] [-n] [-o output_file] [-p mode] [-q] [-s start_file] 
  [-t training_file] [-v]

Options are:

-a Write protein translations to the selected file
-c Closed ends. Do not allow genes to run off edges.
-d Write nucleotide sequences of genes to the selected file.
-f Select output format (gbk, gff, or sco). Default is gbk.
-g Specify a translation table to use (default 11).
-h Print help menu and exit.
-i Specify input file (default reads from stdin).
-m Treat runs of n's as masked sequence and do not build genes across them.
-n Bypass the Shine-Dalgarno trainer and force the program to scan for motifs.
-o Specify output file (default writes to stdout).
-p Select procedure (single or meta). Default is single.
-q Run quietly (suppress normal stderr output).
-s Write all potential genes (with scores) to the selected file.
-t Write a training file (if none exists); otherwise, read and use the specified training file.
-v Print version number and exit.