Beginning Perl for Bioinformatics
January 16th, 2010 | 
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With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you’re a biologist with little or no programming experience, starting out in Perl can be a challenge. Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises. By the end of the book you’ll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming.Amazon.com Review
Biology, it seems, is a good showcase for the talents of Perl. Newcomers to Perl who understand biological information will find James Tisdall’s Beginning Perl for Bioinformatics to be an excellent compendium of examples. Teachers of Perl will likewise find the text to be filled with fresh programming illustrations of growing scientific importance. Seasoned Perlmongers who want to learn biology, however, should search elsewhere, as Tisdall’s emphasis is on Perl’s logic rather than Mother Nature’s.
Departing from O’Reilly’s earlier monograph Developing Bioinformatic Computer Skills, Tisdall’s text is organized aggressively along didactic lines. Nearly all of the 13 chapters begin with twin bullet lists of Perl programming tools and the bioinformatic methods that require them. Likewise, the chapters end with exercises. String concatenation is illustrated with gene splicing, and regular expressions are taught with gene transcription and motif searching.
Tisdall emphasizes sequence examples throughout, leading up to an introduction to a Perl interface for the NIH GenBank biological database and the widely used BLAST sequence alignment tool. After a brief discussion of three-dimensional protein structure, he returns to sequence extraction and secondary structure prediction.
Tisdall’s goal is to boost the beginning programmer into a domain of self-learning. He imparts essential etiquette for the success of programming newbies: use the wealth or resources available, from user documentation to Web site surveys to FAQs to How-To’s to news groups and finally to direct personal appeals for help from a senior colleague. A well-plugged-in bioinformatics Perl student will soon discover Bioperl, an open-source effort to bring research-grade bioinformatic tools to the Perl community. Bioperl is described briefly at the end of Tisdall’s book and will reportedly be a forthcoming title of its own in the O’Reilly bioinformatics series.
Although he introduces bioinformatics as an academic discipline, Tisdall treats it as a trade throughout his book. He indicates that open questions and computational hard problems exist, but does not describe what they are or how they are being tackled. Ultimately, Tisdall presents bioinformatics as another arrow in a bench scientist’s quiver, very much like HPLC, 2D-PAGE, and the various spectroscopies.
As odd as a “bioinformatics-as-tool” book may be to its research proponents, the reduction of bioinformatics to trade status both deflates and vindicates the years of research, as Tisdall’s work attests. –Peter Leopold
Beginning Perl for Bioinformatics
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5 Responses to “Beginning Perl for Bioinformatics”
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This book manages to be an astounding introduction to actually using Perl in general as well as a good introduction to its use in bioinformatics. It’s also very readable. Needs more than 5 stars!
Rating: 5 / 5
One can enjoyably learn some Perl and genomics from Tisdall, but a more thorough approach is first using a dedicated Perl primer, like Pierce’s ,Teach Yourself Perl in 24 Hours, or Schwartz & Chistiansen’s, Learning Perl, and then studying the professional toolkit in Dwyer’s Genomic Perl which is accompanied by 65 intuitively derived programs and modules.
Rating: 3 / 5
I liked this book because I had very little background in programming (aside from a semester of C++ a long time ago) and it wasn’t too overwhelming. The excercies were great and the programming was explained fairly well.
I did a lot of bio-informatic work (lineplots, blasts, etc). The book was great for teaching programming that would be useful for these applications, and not a lot of other miscellaneous programming, that i would never really need.
Rating: 5 / 5
I have used this book in a beginning Perl programming course for biology majors. While it is good if you sift through it from start to the end, I often found it impossible to find things when I needed to go back to remind myself of something. The index does not help, and there is no concise language reference anywhere.
Also, I do not like the fact that it uses “quick and dirty” Perl (no “use strict” pragma). While it might be less confusing to skip it at the very beginning, very soon students start to waste too much precious class time trying to locate bugs that would make the program not compile with “use strict” in the first place (e.g. mistyped variable names).
Rating: 3 / 5
If you haven’t programmed in perl before, this book is perfect for learning. It also teaches very low level bioinformatics skills that’d probably help an undergraduate get their next internship. I was clueless to perl, and programming for that matter, when I got this book a long time ago. I painfully flipped each page from front to back, because it ‘is’ a technical book, and absorbed everything as much as possible. This book set me off in a direction that I never imagined. Although we’re on the brink of version six of the language, this book will do you right in any aspect of computer programming. For a ‘beginner’ looking to get into any language, this book is for you. It’s painful, but try and take the time to really learn the information the book presents. It not only teaches you perl, but gives you a peek into the numerous databases and resources that exist as well as a terrific job of teaching you how to use regular expressions.
In the end, you’ll have the foundation to become whatever kind of perl programmer you desire. If you’re looking into bioinformatics, or a bioinformatician looking to learn, I recommend this book as well as ‘Programming Perl’, ‘Mastering Perl for Bioinformatics’, and ‘BLAST’. ‘BLAST’ is fairly easy to breeze through and does a good job of explaining everything you would need to know. ‘Mastering Perl…’ picks up where this book left off, and ‘Programming Perl’ is one of the best buys I ever made, in regards to perl. I know these are all O REILLY books, but they’re probably the best source for perl books out there. I’m not pitching their books either. Lastly, if you have the time I recommend you crunch on through ‘CGI Programming with Perl’. Although the book is a bit out of date, it’s definitely another ‘piece’ of the puzzle for someone to become a LAMP programmer.
Rating: 5 / 5