NAME
prodigal - microbial (bacterial and archaeal) gene finding program
SYNOPSIS
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]
DESCRIPTION
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.