prodigal(1)
microbial (bacterial and archaeal) gene finding program
Description
PRODIGAL
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
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-a: |
Write protein translations to the selected file. | ||
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-c: |
Closed ends. Do not allow genes to run off edges. | ||
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-d: |
Write nucleotide sequences of genes to the selected file. | ||
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-f: |
Select output format (gbk, gff, or sco). Default is gbk. | ||
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-g: |
Specify a translation table to use (default 11). | ||
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-h: |
Print help menu and exit. | ||
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-i: |
Specify input file (default reads from stdin). | ||
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-m: |
Treat runs of n’s as masked sequence and do not build genes across them. | ||
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-n: |
Bypass the Shine-Dalgarno trainer and force the program to scan for motifs. | ||
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-o: |
Specify output file (default writes to stdout). | ||
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-p: |
Select procedure (single or meta). Default is single. | ||
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-q: |
Run quietly (suppress normal stderr output). | ||
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-s: |
Write all potential genes (with scores) to the selected file. | ||
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-t: |
Write a training file (if none exists); otherwise, read and use the specified training file. | ||
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-v: |
Print version number and exit. |