prodigal1
Microbial (bacterial and archaeal) gene finding program
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]
Overview
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.
Options
-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.
Releases
Unchanged in 6 releases since Debian 8 (Jessie).