Perl in bioinformatics
Part 4. Bioinformatics
4.8. Modern Programming Paradigms in Biology
Short Specialist Review
Published Online: 15 NOV 2005
Copyright © 2005 John Wiley & Sons, Ltd
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.
- 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;
- sequence analysis