prodigal(1) microbial (bacterial and archaeal) gene finding program


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]


Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.


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