Comparing coronavirus SARS-CoV-2 spike protein sequences with BioPerl

Continuing from extraction of coronavirus spike protein sequences I decided to compare them and see if any mutations could be found. To do this I needed to align sequences to each other and get multiple sequence alignment. There are many tools that might be used and I have chosen MUSCLE as it is fast, easy to use and accurate enough. However,…

Extracting coronavirus SARS-CoV-2 spike protein sequences with BioPerl

As I started learning Perl I found out that there is a collection of Perl modules for bioinformatics tasks and it is called BioPerl. Intrigued I decided to try to use it for a simple task as it would help me in learning Perl. So the next question was: what task should I choose? Maybe download file with biological sequences, parse it and filter according some criteria? Thinking about this further I made a choice. I will work with sequences of infamous coronavirus which is more precisely named as /var/www/users/zubenel/index.html

Struggle getting PDL book example to work on Windows 10

Encouraged by Enkidu I decided to write a little about my unsuccessful trial to run PDL Book example on Windows. It all started in December 2019 as I decided to learn Perl and looked for a way to create SVM (Support Vector Machine) model with it as I am able to do similar tasks in R or Python. As a side effect and to my surprise I have found that there exists such a thing as Perl Data Language (PDL) that has many modules suited for data science.

Intrigued by PDL I have installed Strawberry Perl 5.…