Installing ProtParam on Ubuntu using Julia and analyze multiple sequences

ProtParam standalone

“ProtParam” is a tool available as web service for calculation of Protein parameters, such as Molecular weight, Extinction coefficient, … However, the usage via the webserver is not very handy if many sequences have to be processed. Therefore, a guide how to download “ProtParam” and to run it via its programming language “Julia” on Linux Ubuntu with multiple sequences will be provided.

Installation of Julia on Ubuntu

Two ways how to install Julia:

1. Type the command provided from the Julia webpage:

curl -fsSL https://install.julialang.org | sh

Small hint: Once you have to press enter while this script is running.

2. Download “Julia” and unpack it by typing:

tar -xvf julia-1.5.1-linux-x86_64.tar.gz

change the name according to the current version

• Move the extracted directory to a folder you want to store “Julia”

mv julia-1.5.1/ xxx

for instance in your home folder under ~/programs/

• Add a symbolic link to the main path of your system for command-line execution

sudo ln -s ~/programs/julia-1.5.1/bin/julia /usr/local/bin/julia

• With that “Julia” should be executable, try by open a terminal and typing julia

Installation of ProtParam via Julia

• “ProtParam” is available as GitHub repository and be directly added to Julia via its package manager.
• Within “Julia” install ProtParam via the Pkg function.

import Pkg

pkg.add(url="https://github.com/zmactep/ProtParam.jl.git")

• BioSequences can be installed with the correct version by:

]# within Julia press <alt + bracket> to switch to the package manager.

add BioSequences@2.0.5

Hint: Removing other versions of BioSequences works with:

rm BioSequences

• For BioSequences only the version 2.0.5 is working!
• After installation, “ProtParam” can be found under ~/.julia/ProtParam/ and can be used within "Julia".

Usage of ProtParam

• First the modules have to be loaded in “Julia”.

using ProtParam

using BioSequences

The first time julia has to compile it, which takes some seconds...

• To process a sequence you can define a variable.

sequence = aa"MYSEQENCE"

protparam(sequence)

• The output should look like this:

Batch Mode

• It is also possible to run “ProtParam” and “Julia” via a batch script.
• Therefore create a file (protParam.run) containing following input:

#!/usr/local/bin/julia

using ProtParam

using BioSequences

sequence = aa"MYSEQENCE"

println(protparam(sequence))

• The requirement is that the “Julia” executable is in you path as mentioned above and that the protParam.run file is executable (chmod +x protParam.run).

Wrapper for analysis of multiple sequences

• protParamWrap is a bash script to submit as many sequences as needed and is available for free via its GitHub repository.
• The program can be executed in a linux bash shell, which allows usage under Linux, Mac and Windows10 WSL.

Workflow

• First, the .fasta file is separated into single files.
• Second, .protParam.jl julia files are generated for each sequence.
• Third, .jl files are processed by julia and protParam
• Lastly, results are saved in the summary.txt file

Important: Only pI, Molecular weight, number of Amino acids and Instability Index values are saved.
However, of course more data can be extracted from the results of protParam by adding more variables in the getData function (requires some basic bash scripting knowledge)