How To Install update_blastdb.pl on Ubuntu 22.04

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install ncbi-blast+

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is update_blastdb.pl and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 22.04. This guide was written specifically with a server running Ubuntu 22.04 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install update_blastdb.pl on Ubuntu 22.04. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install update_blastdb.pl using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install update_blastdb.pl using apt by running the following command:

sudo apt -y install ncbi-blast+

Install update_blastdb.pl using apt

Because update_blastdb.pl is available in Ubuntu 22.04’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

After updating apt database, You can install update_blastdb.pl using apt by running the following command:

sudo apt -y install ncbi-blast+

Install update_blastdb.pl 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 22.04. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install update_blastdb.pl by running the following command:

sudo aptitude -y install ncbi-blast+

How to upgrade (update) a single package update_blastdb.pl using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the update_blastdb.pl, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install ncbi-blast+

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install ncbi-blast+

How To Uninstall update_blastdb.pl from Ubuntu 22.04

To uninstall only the update_blastdb.pl package you can execute the following command:

sudo apt-get remove ncbi-blast+

Uninstall update_blastdb.pl and all its dependencies

To uninstall update_blastdb.pl and its dependencies that are no longer needed by Ubuntu 22.04, you can use the command below:

sudo apt-get -y autoremove ncbi-blast+

Remove update_blastdb.pl with all configurations and data

To remove update_blastdb.pl configuration and data from your system you can run the following purge command:

sudo apt-get -y purge ncbi-blast+

Remove update_blastdb.pl completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to update_blastdb.pl package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge ncbi-blast+

Extra info and code examples

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service.

Conclusion

You now have a full guide on how to install update_blastdb.pl using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the update_blastdb.pl from Ubuntu 22.04.

See also: