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Bioinformatics Programming

Linux ‘sed’ command in Perl programming

in Bioinformatics Programming by

When it comes to handling large data files to process, it becomes very difficult to write programs for the beginners, especially when you have to execute another script within one. For this purpose, Linux operating system offers several advantages for bioinformatics programming such as ‘awk’ and ‘sed’ one-liners, they prove to be of great help! Continue reading “Linux ‘sed’ command in Perl programming” »

How to execute Unix/shell commands in a Perl script?

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BioPerl is a collection of Perl modules which is used to write Perl scripts applied in bioinformatics [1]. It is used in bioinformatics programmings such as in developing source codes, standalone software/tools, and algorithms. It’s easy to install and provide various modules which make it easier to execute different functions. However, Python is mostly preferred over the Perl language, still, some of the bioinformatics software is based on Perl such as the standalone version of I-TASSER. Sometimes, it’s big trouble to execute some Unix/shell commands in Perl script for the beginners, it’s difficult to decide which function would be specific to a condition. Therefore, this article is a guide for the execution of Unix/shell commands in Perl script. Continue reading “How to execute Unix/shell commands in a Perl script?” »

What is Numerical Taxonomy? How is it useful?

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Classification of biological species is one of the important concern while studying taxonomic and or evolutionary relationships among various species. Classification is either based on only one / a few characters known as “Monothetic”, or based on multiple characters known as “Polythetic”. Continue reading “What is Numerical Taxonomy? How is it useful?” »

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