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Perl in bioinformatics

Part 4. Bioinformatics

4.8. Modern Programming Paradigms in Biology

Short Specialist Review

  1. R. Hannes Niedner1,
  2. T. Murlidharan Nair1,
  3. Michael Gribskov2

Published Online: 15 NOV 2005

DOI: 10.1002/047001153X.g409321

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Niedner, R. H., Nair, T. M. and Gribskov, M. 2005. Perl in bioinformatics. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.8:104.

Author Information

  1. 1

    University of California, San Diego, CA, USA

  2. 2

    Purdue University, West Lafayette, IN, USA

Publication History

  1. Published Online: 15 NOV 2005


Bioinformatics evolved as a discipline that applies techniques from math, computer science, and statistics to make sense of the vast amounts of data produced by high-throughput experiments in biology. These data are frequently output as experiment-specific text files, which need to be parsed from and to a variety of formats to be amenable to further computational analyses. This process often involves accessing of additional information from on-line repositories, reading and writing to and from files and databases, and ultimately the presentation of results on the World Wide Web.

Perl stands for Practical Extraction and Report Language, and was developed as a UNIX glue language by Larry Wall in the mid-1980s. It has proven to be a powerful tool for the tasks outlined above. Since its inception, Perl has grown far beyond its original use as a text-parsing tool into a fully featured high-level programming language. In this article, we give an overview on how this versatile language can be used to tackle a wide variety of frequent problems in bioinformatics.


  • programming language;
  • genomics;
  • bioinformatics;
  • sequence analysis