How To Install prodigal on Debian 9
Introduction
In this tutorial we learn how to install prodigal on Debian 9.
What is prodigal
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.
There are three methods to install prodigal on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install prodigal Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install prodigal using apt-get by running the following command:
sudo apt-get -y install prodigal
Install prodigal Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install prodigal using apt by running the following command:
sudo apt -y install prodigal
Install prodigal Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install prodigal using aptitude by running the following command:
sudo aptitude -y install prodigal
How To Uninstall prodigal on Debian 9
To uninstall only the prodigal package we can use the following command:
sudo apt-get remove prodigal
Uninstall prodigal And Its Dependencies
To uninstall prodigal and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove prodigal
Remove prodigal Configurations and Data
To remove prodigal configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge prodigal
Remove prodigal configuration, data, and all of its dependencies
We can use the following command to remove prodigal configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge prodigal
Dependencies
prodigal have the following dependencies:
References
Summary
In this tutorial we learn how to install prodigal package on Debian 9 using different package management tools: apt, apt-get and aptitude.