How To Install fasta3 on Ubuntu

Posted on April 1, 2023  (Last modified on May 20, 2023 )

3 minutes  • 506 words

Introduction

In this tutorial we learn how to install fasta3 on Ubuntu.

What is fasta3

fasta3 is:

The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

• Protein

  • Protein-protein FASTA
  • Protein-protein Smith-Waterman (ssearch)
  • Global Protein-protein (Needleman-Wunsch) (ggsearch)
  • Global/Local protein-protein (glsearch)
  • Protein-protein with unordered peptides (fasts)
  • Protein-protein with mixed peptide sequences (fastf)

• Nucleotide

  • Nucleotide-Nucleotide (DNA/RNA fasta)
  • Ordered Nucleotides vs Nucleotide (fastm)
  • Un-ordered Nucleotides vs Nucleotide (fasts)

• Translated

  • Translated DNA (with frameshifts, e.g. ESTs) vs Proteins (fastx/fasty)
  • Protein vs Translated DNA (with frameshifts) (tfastx/tfasty)
  • Peptides vs Translated DNA (tfasts)

• Statistical Significance

  • Protein vs Protein shuffle (prss)
  • DNA vs DNA shuffle (prss)
  • Translated DNA vs Protein shuffle (prfx)

• Local Duplications

  • Local Protein alignments (lalign)
  • Plot Protein alignment “dot-plot” (plalign)
  • Local DNA alignments (lalign)
  • Plot DNA alignment “dot-plot” (plalign)

This software is often used via a web service at the EBI with readily indexed reference databases at http://www.ebi.ac.uk/Tools/fasta/.

There are three methods to install fasta3 on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install fasta3 Using apt-get

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

sudo apt-get update

After updating apt database, We can install fasta3 using apt-get by running the following command:

sudo apt-get -y install fasta3

Install fasta3 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install fasta3 using apt by running the following command:

sudo apt -y install fasta3

Install fasta3 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 fasta3 using aptitude by running the following command:

sudo aptitude -y install fasta3

How To Uninstall fasta3 on Ubuntu

To uninstall only the fasta3 package we can use the following command:

sudo apt-get remove fasta3

Uninstall fasta3 And Its Dependencies

To uninstall fasta3 and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove fasta3

Remove fasta3 Configurations and Data

To remove fasta3 configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge fasta3

Remove fasta3 configuration, data, and all of its dependencies

We can use the following command to remove fasta3 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge fasta3

Dependencies

fasta3 have the following dependencies:

• libc6
• python3

References

• fasta3 website

Summary

In this tutorial we learn how to install fasta3 package on Ubuntu using different package management tools: apt, apt-get and aptitude.