Essentially, Perl is an interpreted programming language that is easily grasped by newcomers in the bioinformatics field. Additionally, it not only connects software applications together into sequence analysis pipelines, but it also converts file formats and extracts information from the output of analyzed programs. Moreover, Perl/Bio-Perl: A Bioinformatics toolkit is a collection of Perl modules that provides an easy-to-use, stable, and consistent interface for bioinformatics application programmers. Furthermore, it is an open-source software project supported by the Open Bioinformatics Foundation. Bioperl was started in 1995 by a group of scientists who were tired of rewriting BLAST and sequence parsers for various formats. Since 1998, Bioperl has been used worldwide in both small academic labs and large pharmaceutical companies. Finally, it is the oldest and most downloaded package among bioinformatics packages currently in use

What makes Bioperl so useful for Bioinformatics???

Firstly, Bioperl offers a wide range of utilities for biological and bioinformatics analysis, including databases and analysis routines for genomics, proteomics, and evolutionary studies. Additionally, Bioperl can analyze results from popular bioinformatics programs like BLAST, Tcoffee, GenScan, and ClustalW.

Furthermore, Bioperl allows users to assess sequences from local and remote databases, transform database/file record formats, manipulate individual sequences, search for similar sequences, create and manipulate sequence alignments, search for genes and other structures on genomic DNA, and develop machine-readable sequence annotations. These features make Bioperl a valuable tool for bioinformatics analysis.

Use Of Perl-Bioperl

Firstly, The Bioperl modules have been used to reduce otherwise complex tasks to only a few lines of code. Second,  The best solution for bioinformatics problems is a hybrid of multiple tools. Third, These tools written in different programming languages like C, Java and Python, can be used in a Perl program simply by invoking them. Fourth, Bioperl provides a software layer that can populate a database with the sequence information that can be assessed and used to generate an interactive graphical interface provided by the Biojava toolkit.

Application of Perl-Bioperl

First Bioperl will perform better than Biojava when processing small data set. Second It is very powerful for string manipulation, compared to Biopython and Biojava. It requires the shortest lines of source code as compared to Biopython and Biojava. Lastly  In the future Bioperl will continue to evolve, addressing more aspects of bioinformatics.


  1. First Stajich, Jason E., David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen et al. “The Bioperl toolkit: Perl modules for the life sciences.” Genome research12, no. 10 (2002).
  2. Second Ryu, Tae-Wan. “Benchmarking of BioPerl, Perl, BioJava, Java, BioPython, and Python for primitive bioinformatics tasks and choosing a suitable language.” International Journal of Contents5, no. 2 (2009).
  3. Third Crossman, Colin, and Arti K. Rai. “A Brief History of BioPerl.” (2005).

You can also check out our more about our bioinformatics course and research services related to Bioinformatics.

WhatsApp chat