How To Install sim4db on Debian 9

Introduction

In this tutorial we learn how to install sim4db on Debian 9.

What is sim4db

sim4db is:

Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package ’leaff’, to speedily process large volumes of sequences.

While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.

This package is part of the Kmer suite.

There are three methods to install sim4db 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 sim4db Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install sim4db using apt-get by running the following command:

sudo apt-get -y install sim4db

Install sim4db Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install sim4db using apt by running the following command:

sudo apt -y install sim4db

Install sim4db 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 sim4db using aptitude by running the following command:

sudo aptitude -y install sim4db

How To Uninstall sim4db on Debian 9

To uninstall only the sim4db package we can use the following command:

sudo apt-get remove sim4db

Uninstall sim4db And Its Dependencies

To uninstall sim4db and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove sim4db

Remove sim4db Configurations and Data

To remove sim4db configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge sim4db

Remove sim4db configuration, data, and all of its dependencies

We can use the following command to remove sim4db configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge sim4db

Dependencies

sim4db have the following dependencies:

• libc6
• libgcc1

References

• sim4db website

Summary

In this tutorial we learn how to install sim4db package on Debian 9 using different package management tools: apt, apt-get and aptitude.