RNAsnoop command not found

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

Introduction

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

RNAsnoop: command not found

or when using sudo you get the following error message

sudo: RNAsnoop: command not found

Solutions to RNAsnoop: command not found

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

In Ubuntu RNAsnoop is provided by vienna-rna package.

vienna-rna is:

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna.

RNA secondary structure prediction through energy minimization is the most used function in the package. It provides three kinds of dynamic programming algorithms for structure prediction:

  • the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure,
  • the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy.

For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, is provided an algorithm to design sequences with a predefined structure (inverse folding). The RNAforester package is a tool for aligning RNA secondary structures and it’s user interface integrates to those of the tools of the Vienna RNA package.

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

sudo apt-get -y install vienna-rna

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

You can also use apt command to install vienna-rna.

sudo apt -y install vienna-rna

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

sudo aptitude install vienna-rna

Summary

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