sim4 command not found

Introduction

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

sim4: command not found

or when using sudo you get the following error message

sudo: sim4: command not found

Solutions to sim4: command not found

How To Fix sim4: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu sim4 is provided by sim4 package.

sim4 is:

sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).

sim4 employs a blast-based technique to first determine the basic matching blocks representing the “exon cores”. In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.

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

sudo apt-get -y install sim4

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

You can also use apt command to install sim4.

sudo apt -y install sim4

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

sudo aptitude install sim4

Summary

In this tutorial we learn how to fix sim4 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.