prodigal - 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.
- -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.