ssearch36 command not found

In this troubleshooting guide we learn how to fix ssearch36 command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

ssearch36: command not found

or when using sudo you get the following error message

sudo: ssearch36: command not found

Solutions to ssearch36: command not found

How To Fix ssearch36: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu ssearch36 is provided by fasta3 package.

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/.

To fix this problem, we can install more using the command below.

sudo apt-get -y install fasta3

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install fasta3.

sudo apt -y install fasta3

Or if you have aptitude installed you can use the following command.

sudo aptitude install fasta3

Summary

In this tutorial we learn how to fix ssearch36 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.