Pittsburgh Supercomputing Center 

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Prodigal

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

Installed on blacklight and  biou.

Other resources that may be helpful include:

  • 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.
  • Website: http://prodigal.ornl.gov/

Running Prodigal

On blacklight

The Prodigal programs are made available for use through the module command. To load the Prodigal module enter:

module load prodigal

On biou

The Prodigal programs are availiable through the Galaxy instance on biou.

To make the Prodigal programs availiable through the command line, csh users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

To make the Prodigal programs availiable through the command line, bash users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

Prodigal 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.