prodigal command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

prodigal: command not found

or when using sudo you get the following error message

sudo: prodigal: command not found

Solutions to prodigal: command not found

How To Fix prodigal: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu prodigal is provided by prodigal package.

prodigal is:

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. Key features of Prodigal include:

Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.

Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3’ end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5’ ends in the Ecogene data set are located correctly).

Specificity: Prodigal’s false positive rate compares favorably with other gene identification programs, and usually falls under 5%.

GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5’+3’) to the Pseudomonas aeruginosa curated annotations.

Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.

Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.

To fix this problem, we can install more using the command below.

sudo apt-get -y install prodigal

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install prodigal.

sudo apt -y install prodigal

Or if you have aptitude installed you can use the following command.

sudo aptitude install prodigal

Summary

In this tutorial we learn how to fix prodigal command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.