How To Install ncbi-epcr on Ubuntu 18.04
Introduction
In this tutorial we learn how to install ncbi-epcr on Ubuntu 18.04.
What is ncbi-epcr
ncbi-epcr is:
Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.
The new version of e-PCR implements a fuzzy matching strategy. To reduce likelihood that a true STS will be missed due to mismatches, multiple discontiguous words may be used instead of a single exact word. Each of this word has groups of significant positions separated by ‘wildcard’ positions that are not required to match. In addition, it is also possible to allow gaps in the primer alignments.
The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database.
This program is retired upstream and it is suggested to use Primer-Blast https://www.ncbi.nlm.nih.gov/tools/primer-blast/ instead.
There are three methods to install ncbi-epcr on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install ncbi-epcr Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install ncbi-epcr using apt-get by running the following command:
sudo apt-get -y install ncbi-epcr
Install ncbi-epcr Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install ncbi-epcr using apt by running the following command:
sudo apt -y install ncbi-epcr
Install ncbi-epcr 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install ncbi-epcr using aptitude by running the following command:
sudo aptitude -y install ncbi-epcr
How To Uninstall ncbi-epcr on Ubuntu 18.04
To uninstall only the ncbi-epcr package we can use the following command:
sudo apt-get remove ncbi-epcr
Uninstall ncbi-epcr And Its Dependencies
To uninstall ncbi-epcr and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove ncbi-epcr
Remove ncbi-epcr Configurations and Data
To remove ncbi-epcr configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge ncbi-epcr
Remove ncbi-epcr configuration, data, and all of its dependencies
We can use the following command to remove ncbi-epcr configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge ncbi-epcr
References
Summary
In this tutorial we learn how to install ncbi-epcr package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
