1) The document discusses programming languages for bioinformatics and why Perl is particularly well-suited for tasks in the field. 2) Perl is free, cross-platform, easy to write and develop quickly in, and good for prototyping algorithms before moving to other languages. 3) The document lists six reasons Perl has become widely used in bioinformatics, including its abilities to manipulate text-based biological data and its forgiving nature given incomplete biological data fields.

1. OK INBRE Bioinformatics Bulletin
University of Oklahoma Health Sciences Center
December 2006
Programming for Bioinformatics
by Timothy Schmidt, M.S.
In previous versions of this newsletter, we have Pascal, C, C++, and Java programming languages have
focused on some of the common bioinformatic tools been widely implemented since that time.
available to the budding bioinformatician. These, and The bad news is, these programming languages
many other applications, could be thought of as the typically can, and do, take an extensive amount of time
“core” of bioinformatics, and certainly a great deal can to learn and master. Furthermore, building a “full­
be accomplished solely with them. But what happens featured” application can take years, an investment the
when you need to address a question for which an typical researcher will have no interest in making. What
application does not exist? It’s not a surprising or rare is frequently needed bioinformatics, however, isn’t a
occurrence; original research projects often require full featured elaborate program with a stylistic graphical
original analyses. And perhaps just as importantly, user interface (GUI), but a simple, efficient, and
many situations in the modern biology lab require accurate method to manipulate data for use in other
manipulation of very large datasets in order to process applications. Fortunately a programming language
data for use in core applications and to help organize (Perl) exists that is particularly well suited for these
and interpret the results emanating from them. In these tasks.
circumstances it is useful for a biologist to have at least
some basic programming skills at their disposal. Apart Perl
from these (often lab­specific) tasks, programming can Perl stands for Practical Extraction and
also open up to broader applications for use by the Reporting Language. Perl has gained widespread usage
general biological community. in the maintenance and production of Web site, and has
become known as the “duct tape of the Internet”. One
Programming languages aspect of content for the internet, the broad use and
The purpose of a programming language is to manipulation of text, is also a reason that Perl has been
instruct computers on how to perform tasks. so readily put to use in bioinformatics. The genetic
Programming languages differ from other languages in code, DNA sequence, Genbank data files, PDB (protein
the level of specificity required. The reason for their database) files, etc., are all based on text (as opposed to
rigid structure is that the target of the communication (a numerical) data.
machine) is unable to “intuit”, and even very small Perl is also more readily taken up than other
trivial errors can have disastrous effects. There are programming languages, which are stricter and more
literally thousands of computer languages, with new structured. “There’s more than one way to do it”
ones being introduced each year, but there have been (TMTOWTDI) is another common Perl acronym. The
only a few that have gained widespread usage. The first leniency in Perl coding structure can be a huge time­
widely used language was FORTRAN, which was good saver, but it also has costs. It is sometimes nearly
at handling numeric data, but COBOL was impossible to debug or modify another programmer’s
subsequently developed for business applications. The code, leading some to refer to it as the Pathologically

2. Bulletin (continued)
The University of
Oklahoma Health Eclectic Rubbish Lister. But the best 3) Perl is component­oriented; 4) Perl
Sciences Center description of Perl may be that it is the is easy to write and fast to develop in;
Swiss Army chainsaw of programming 5) Perl is a good prototyping
languages. language… it often makes sense to
prototype new algorithms in Perl
Laboratory for Genomics and Perl for Bioinformatics before moving them to a fast compiled
Bioinformatics
Perl has many other advantages language; and 6) Perl is a good
Edgar Scott II, M.S.
Multicampus Bioinformatics Education that has endeared it to language for Web CGI scripting, and is
Specialist
bioinformaticians. It’s free, and growing in importance as more labs
Phone:
(405) 271-2133 x32511 available for almost any platform turn to the Web for publishing their
E-Mail:
edgar-scott@ouhsc.edu
(Mac, Windows, Linux, etc.). data.
Programs that are written on the Mac Because of Perl’s popularity
will work in Windows, etc. This has a there are many resources available on
cost… Perl has very little in the way of the Web, and most can be found
a GUI and is predominantly used from through www.bioperl.org and
the command line. Very few “point and www.perl.com. The latter is a site
click” types of applications are maintained by O’Reilly & Associates,
We’ re on the Web! who publish the books “Beginning Perl
produced with Perl, although they can
See us at: be created with “helper” applications, for Bioinformatics”, and “Mastering
http://microgen.ouhsc. such as Perl2Exe. Perl for Bioinformatics” by James
edu/inbre/ In “How Perl saved the human Tisdall. You can also find links to
genome project”1, Lincoln Stein listed download Perl for Mac and Windows
six reasons that Perl has become the at this site (Perl comes standard in
most widely used programming Linux distributions). Finally, there are
language of bioinformatics: 1) Perl is numerous sites with tutorials on how to
remarkably good for slicing, dicing, begin learning Perl throughout the
Website Reference twisting, wringing, smoothing, Web, and googling for “Perl tutorial”
summarizing and otherwise mangling should get you started on the path to
1.http://www.bioperl.org/wiki/How_
Perl_saved_human_genome
text… Perl's powerful regular programming in Perl!
expression matching and string
manipulation operators simplify this
job in a way that isn't equaled by any
other modern language; 2) Perl is
forgiving…biological data is often
incomplete, fields can be missing, etc.;
About Us…
The OUHSC Laboratory for Genomics and Bioinformatics is a full-service genomics facility offering DNA sequencing (small- and large-scale
projects), microarray design and hybridization and other services, including bioinformatics support. Edgar Scott is the INBRE Multicampus
Bioinformatics Education Specialist, responsible for fostering the development of bioinformatics education on 14 undergraduate campuses in
the state of Oklahoma, and coordinating INBRE-related bioinformatics activities with the INBRE Bioinformatics Core. The University of
Oklahoma is an equal opportunity institution. This publication is printed and issued by the University of Oklahoma; the cost of $150 was paid
by OK INBRE.