fasta_to_raw command not found

Introduction

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

fasta_to_raw: command not found

or when using sudo you get the following error message

sudo: fasta_to_raw: command not found

Solutions to fasta_to_raw: command not found

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

In Ubuntu fasta_to_raw is provided by pscan-chip package.

pscan-chip is:

Regulation of transcription is one of the main check points of gene expression regulation and plays a key role in fundamental processes like cellular differentiation and dynamic molecular responses to stimuli The transcriptional activity of genes is finely regulated by the interaction of sequence elements on the DNA (transcription factor binding sites or TFBSs) and particular proteins called Transcription Factors (TFs). , TFBSs are usually clustered in specific regulatory genomic regions called promoters and enhancers. TFs usually recognize TFBSs in a loose sequence specific fashion but there is no computational way to determine if any given sequence motif on the DNA is actually bound in-vivo by a TF, even when the motif is an istance of the sequences typically bound by the TF itself.

Tools like Pscan and PscanChIP analyse a set of regulatory sequences to detect motif enrichment. The rationale is that if a given TFBS is present in a “surpisingly high” number of istances then there is a good chance that the TF that recognize that motif is a common regulator of the input sequences, thus they use redundancy as an information source.

While Pscan (of the pscan-tfbs package) is tailored to work on promoters, that is the regulatory regions upstream of transcription start sites, PscanChIP is suited to work on more general regulatory genomic regions like the ones identified through ChIP-Seq experiments.

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

sudo apt-get -y install pscan-chip

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

You can also use apt command to install pscan-chip.

sudo apt -y install pscan-chip

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

sudo aptitude install pscan-chip

Summary

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