Beginning Perl for Bioinformatics

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

Product Description
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.

Since it is addressed to readers with no programming experience, the author introduces some elementary concepts of programming in the first three chapters. These include what text editor to use, how to install PERL, how run PERL programs, and other relevant elementary topics.

The author then gets down to writing a program to store a DNA sequence in chapter 4. Very basic, it merely reads in a string and prints it out, but serves to start readers on their way to developing more useful programs. Later a program for the transcription of DNA to RNA is given, which illustrates nicely the binding, substitution and trace operators. Block diagrams are used here, and throughout the book, to illustrate basic PERL operators. The author shows in detail how to read protein sequence data from a file and how to use it in a PERL program. The reader is also introduced to the most ubiquitous data structure in all of computing: the array. Already the reader gets a taste of the power of PERL to manipulate arrays, using operations such as 'unshift', 'push', 'splice', etc.

The next chapter introduces conditional statements in PERL, as a warm-up for the discussion on finding motifs in sequences. The reader can see why PERL is the language of choice in bioinformatics, with its ability to find substrings or patterns in strings. Things do become more cryptic in the discussion of regular expressions, but the reader can get through it with some effort. Interesting programs are given for determining the frequency of nucleotides.

Since the programs have become more complicated to this point, a discussion of subroutines follows in the next chapter. And, for the same reason, the reader is introduced to debugging in PERL in this chapter also. The greater the complexity of the program, the harder it becomes to avoid making mistakes, and even more difficult to find them. The very important concepts of pass by value versus pass be reference are discussed briefly in this chapter.

Random number generators, so important in any consideration of mutations, are discussed in chapter 7. It is shown, via some straightforward programs, how to select a random location in DNA and mutate it with some other nucleotide. In addition, the author shows how to use random numbers to generate DNA sequences and mutate them in order to study the effect of mutations over time.

The next chapter is the most interesting in the book, for it shows how PERL can be used to simulate how the genetic code directs the translation of DNA into protein, the hash data structure being used extensively for this purpose. The author shows how to read DNA from files in FASTA format, and discusses in detail reading frames. He gives a useful subroutine to translate reading frames.

The author returns to regular expressions in chapter 9, wherein they are used as 'wildcards' to search for a particular string in a collection of strings. In addition, the range operator is used to find restriction sites. Regular expressions are also used in the next chapter to manipulate GenBank 'flat files'. The author does however give URLs for more sophisticated bioinformatics software. This is followed in chapter 11 by a discussion of the use of PERL to work with files in the Protein Data Bank. Recursion, one of the most powerful techniques in programming, is introduced here.

Chapter 12 covers the Basic Local Alignment Search Tool (BLAST), wherein readers get a taste of the field of computational biology. This extremely popular software package is used to find similarity between a given sequence and a library of known sequences. The author does discuss some of the basic rudiments of string matching and homology, and encourages the reader to consult the BLAST documentation for further details. In addition, the author briefly discusses the Bioperl project in this chapter, and shows the reader how to run some elementary computations using it.

This book definitely is a timely one and it will serve the needs of biologists who need to obtain some programming expertise in PERL. There are helpful exercises at the end of each chapter that serve to solidify the understanding of the concepts introduced in the chapter. After a thorough study of it, readers will be well-equipped to use PERL in bioinformatics. With more mathematical background, readers after finishing it will be able to enter the exciting field of computational biology, a field that is exploding, and one in which will require imaginative programming skill in the future.


A friendly and excellent introduction to perl for biologists   January 10, 2002
John M. Gardner (davis, ca United States)
8 out of 8 found this review helpful

The author presents Perl in a thorough, well organized fashion,always reinforcing the use of the basic tools ...scalars,arrays,hashes, regular expressions,loops and subroutines,parsing data banks,relational databases,perl modules,program design and so on.He presents clearly ,giving many examples of real life biological problems. It assumes little if any programming background, although a knowledge of C and Unix would be very helpful. This is definitely a must for anyone learning Perl for molecular biology. 5 stars ++


No need to have any previous programming knowledge   December 5, 2001
Pine Tree
7 out of 7 found this review helpful

I had zero programming experience when I started reading this book. It allowed me, step by step, to get familiar with the language and start writing programs related to the field I am interested in.
It is fun and very helpful. You don't feel the frustration of being lost in the middle of unreadable code. The comments and explanations to the programs are great. It allows you to start learning the simple things first and then, as you get familiar with the language, go into more detail.
You can chose, as the author suggests, to go sometimes to the Perl documentation and read about the operators or functions introduced in the different programs; but what is great about the book is that you are given examples and exercises to use them. This is really the way to learn.


Good Start   February 27, 2003
Lynn Allen Messinger (Evansville, WI United States)
5 out of 5 found this review helpful

I am a biologist who has written 'Hello World' in innumerable programing languages and progressed no further. No matter how many different books I buy and put on my shelf I still haven't learned to program. After removing this book from the Perl section of my shelf and spending two days with it I wrote a script that turns an amino acid sequence into a degenerate oligo (DNA) and prints its reverse compliment. Certainly not bioinformatics but I impressed myself. This was because simple things that any programmer would know, but I do not, are explained in detail. Thank you. Thank you. Thank you.

Because of this book I am confident that I will now be able to do many of the simple sequence manipulations my current projects require. However and but. A cusory glance at the innards of 'Programming Perl' is enough to show just how much more their is to Perl.

The title is not misleading but it could have been 'Beginning Perl for Beginning Bioinformatics'. Ain't no Hidden Markov models here.

Five stars this time but next time their better be MORE in the same style.


Solid segway into Perl   June 24, 2005
Elliot Kleiman (Los Angeles, CA United States)
5 out of 5 found this review helpful

For those of you who are originally from biology, and now want to/need to venture into the realm of computer programming for biological data, this is a great way to start learning. Its much more than just a basic run-of-the-mill intro programming book however, because the author applies everything towards biology.

In this sense the author first writes code examples with the intention that they can be used in your lab or just further your understanding about programming in general.

From a programming perspective, one of the premier strengths of this particular book is its coverage on Regular Expressions. The author uses the method of drill to explain and explain and break down each segment of any presented regular expression in great detail so that pretty much anyone with a little programming background can understand.

In addition, the chapters are wonderfully presented with not too much but not too little content, but just the right amount.
Probably, the second biggest strength of this book is its organization and layout of each chapter. Well there's that and its awesome index/appendix where you can pretty much find the stuff you are looking for.

I would recommend this book highly to anyone wanting to/needing to use Perl to handle their biological programming needs. Overall, this little book offers much as a solid segway into intro Perl programming for bioinformatics.

Assumptions about the reader:
This is an applied introductory book on Perl for Biology. Although it is introductory it would be best if you the reader had some prior computer programming knowledge under your belt (say in [C/C++/etc,...] to truly understand the material however its not a requirement. The only reason I mention that is because Perl is weird - its lack of strictness (no pun intended on the 'use strict' pragma fyi) can get frustrating at times because there are so many ways to do the same thing in Perl - thats what makes Perl weird IMHO.

The final word:
If you are not a pure programmer-type but a biology person wanting to learn programming - moreover programming in Perl for biology - this is definitely a good book to learn with - I really learned quite a bit from this book on how to parse files using regular expressions, and how to program in Perl. Its an intro-to-intermidiate level programming book thats quite good to begin with - hence the name 'Beginning Perl for Bioinformatics'.