a3m_extract command not found

Introduction

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

a3m_extract: command not found

or when using sudo you get the following error message

sudo: a3m_extract: command not found

Solutions to a3m_extract: command not found

How To Fix a3m_extract: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu a3m_extract is provided by hhsuite package.

hhsuite is:

HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

This package contains HHsearch and HHblits among other programs and utilities.

HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling.

HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.

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

sudo apt-get -y install hhsuite

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

You can also use apt command to install hhsuite.

sudo apt -y install hhsuite

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

sudo aptitude install hhsuite

Summary

In this tutorial we learn how to fix a3m_extract command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.