guest post from Susanne Cardwell,
Administrative Coordinator for the Applied Computational Genomics Course

Perl is a dynamic programming language used in many areas - especially in bioinformatics. It is a freely downloadable and commonly used with Unix systems, although some variants are available for Microsoft Windows.

On perusing notes made for one of the lecture days of the 2009 Applied Computational Genomics Course , I located some interesting information on Perl in bioinformatics. Perl, as used in bioinformatics, allows for a number of operations, including:

• translation of DNA sequences in a single frame
• transcription of DNA to RNA
• production of reverse complements of DNA sequence nomenclature
• coding for aiding RNA splicing
• generation of Blast output
• prediction and evaluation of genes
• annotation of a small genome (such as E. coli) or a collection of EST’s (Wishart, 2009)

MedicineNet, Inc. (2009) defined genome annotation as “the process for identifying the location of genes and all of the coding regions in a genome and determining what those genes do.” For instance, DNA Forensics allows for the identification of organ donor matches and the identification of individuals suspect in a crime through DNA profiling through scans of 13 DNA regions (Human Genome Project Information, 2009). A more specific example of genome annotation is when you determine the function of the gene (such as protein excretion, protein family and transcription identification, and transcription determination (Abdellateef, 2009, December 17, personal communications) and the regions of the gene that would eventually translate into protein. Perl helps allow for complex annotation to take place – annotation that would not otherwise have been possible through traditional means.

For those interested in developing their Perl know-how, a book on Perl recommended on an MIT webpage is called Learning Perl, Third Edition by Tom Phoenix and Randal L. Schwartz (Biocomputing at Whitehead Institute, n.d.).

Abdellateef, M. (2009, December 17). Personal communications.

Biocomputing at Whitehead Institute. (n.d.). WIBR Bioinformatics for Biologistst Lecture 5 & 6
Resources: Computational Methods II, III: Sequence Analysis with Perl (including modules
and BioPerl). Retrieved December 17, 2009, from http://jura.wi.mit.edu/bio/education/bioinfo/pages/perl_bioinfo.html  

Human Genome Project Information. (2009). DNA forensics. Retrieved December 17, 2009, from http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml  

MedicineNet, Inc. (2009). Definition of Genome annotation. Retrieved December 17, 2009, from http://www.medterms.com/script/main/art.asp?articlekey=16833

Wishart, D. (2009). Perl and the Web. Accessed from the notes for the Applied Computational Genomics Course in Montreal, Quebec, July 2009