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Beginning Perl for Bioinformatics [Paperback]

James Tisdall
4.5 out of 5 stars  See all reviews (37 customer reviews)

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Book Description

October 29, 2001 0596000804 978-0596000806 1

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. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.

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 and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. 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. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.

The book covers:

  • Programming basics and working with DNA sequences and strings
  • Debugging your code
  • Simulating gene mutations using random number generators
  • Regular expressions and finding motifs in data
  • Arrays, hashes, and relational databases
  • Regular expressions and restriction maps
  • Using Perl to parse PDB records, annotations in GenBank, and BLAST output

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Beginning Perl for Bioinformatics + Mastering Perl for Bioinformatics + Learning Perl
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Editorial Reviews

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

Book Description

An Introduction to Perl for Biologists

Product Details

  • Paperback: 400 pages
  • Publisher: O'Reilly Media; 1 edition (October 29, 2001)
  • Language: English
  • ISBN-10: 0596000804
  • ISBN-13: 978-0596000806
  • Product Dimensions: 9.6 x 6.4 x 0.8 inches
  • Shipping Weight: 1.2 pounds (View shipping rates and policies)
  • Average Customer Review: 4.5 out of 5 stars  See all reviews (37 customer reviews)
  • Amazon Best Sellers Rank: #57,887 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews
48 of 49 people found the following review helpful
5.0 out of 5 stars Very timely introduction to PERL November 10, 2001
Format:Paperback|Verified Purchase
Finally someone has written a beginning book on PERL for biologists, and has also done an excellent job of doing so. This book assumes no prior programming experience, and therefore suits the biologist who needs to concentrate on using computers to solve biological problems, and not have to become a computer scientist in the process. PERL can be a very cryptic language, but it is also extremely concise, and PERL programmers frequently and rightfully boast about their "one-liners" that accomplish complicated tasks with only one line of code.
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.
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17 of 17 people found the following review helpful
Format:Paperback
"Bioinformatics" is the new sexy term for what used to be called simply "computational biology". Simply put, it involves pretty much any application of computation techniques to biological problems. The reason for the new nomenclature and the greatly increased interest in the topic is, like much in modern biology, a more-or-less direct consequence of the many genome sequencing projects of the last decade.
The consensus in the field seems to be that it's more productive (and certainly easier) to teach biologists how to program, rather than try to get programmers up to speed on the intracities of molecular biology. For similar reasons, Perl is a popular language to learn: it's easy to get off the ground and be productive with it, without requiring a heavy computer science background. (This, of course, has downsides as well...)
Never one to miss out on a trend, I'm going to be teaching a course on Bioperl and advanced Perl programming, starting next fall, which means I'm doing a lot of reading in this topic area, trying to develop lectures and find good background reading material. One of the first books I grabbed was _Beginning Perl for Bioinformatics_, which has been sitting on my "to read" shelf since O'Reilly sent me a review copy in December of 2001. It's a typical O'Reilly "animal" book (the cover bears three tadpoles), which does a decent job of introducing the basic features of the Perl language, and it should enable a dedicated student to get to the point where she can produce small useful programs. However, I'm not completely happy about the book's organization, and I think the occasional "if you're not a biologist, here's some background" interjections could have been cut without hurting anything.
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10 of 10 people found the following review helpful
4.0 out of 5 stars Decent intro to the subject July 26, 2003
Format:Paperback
As the banner above the title of James Tisdall's Beginning Perl for Bioinformatics indicates, this book is 'an introduction to Perl for biologists.' What the banner doesn't mention is that it's also an introduction to biology and bioinformatics for Perl programmers, and it's also an introduction to both Perl *and* biology for people that have never really been exposed to either field. The author has clearly thought a lot about making one book to please these different audiences, and he has pulled it off nicely, in a way that manages to explain basic topics to people learning about each field for the first time while not coming off as condescending or slow-paced to those that might already have some exposure to it.
Superficially, this book isn't all that different from a lot of introductory Perl books: the Perl material starts out with an overview of the language, followed by a crash course on installing Perl, writing programs, and running them. From there, it goes on to introduce all the various language constructs, from variables to statements to subroutines, that any programmer is going to have to get comfortable with. Pretty run of the mill so far. Tisdall starts with two interesting assumptions, though: [1] that the reader may have never written a computer program before, and so needs to learn how to engineer a robust application that will do its job efficiently and well, and [2] that the reader wants to know how to write programs that can solve a series of biological problems, specifically in genetics and proteomics.
As such, there is at least as much material about the problems that a biologist faces and the places she can go to get the data she needs as there is about the issues that a Perl programmer needs to be aware of.
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Most Recent Customer Reviews
5.0 out of 5 stars Awesome for beginners
This book is a perfect learning package. If you are new to perl and searching for a book that will help you learn perl from scratch, then look no more. Read more
Published 9 months ago by GAYATHRI SURESH
3.0 out of 5 stars Not a good introductionary book
I had somewhat mixed feeling about this book. To begin with I am a biologist with some background in programing. I do not think that this book can satisfy any of my needs. Read more
Published 10 months ago by Oleg Agafonov
2.0 out of 5 stars Basic scripting_poor examples and explanations
Teaches basic scripting for managing bioinformatic data. Gave poor examples and explanations for the topics being discussed. I do not recommend this book.
Published 11 months ago by MJR
5.0 out of 5 stars Very cool book
i have study and apply information and Bioinformatic perls is very informative straight to the point well put together must get for basic
Published 19 months ago by William Savigne
3.0 out of 5 stars Needs to be updated!
This book is only good as a second reference for a beginner. I spent far too much time debugging scripts that probably worked in 2001. Read more
Published 24 months ago by Kimist
5.0 out of 5 stars The book is great!
This is not the first time I order books from Amazon. It only takes couple days to arrive. The book is used but it looks new! I really like Amazon!
Published on October 8, 2011 by snowman
5.0 out of 5 stars Good book for the introductory programmer in Bionformatics
I have a MS degree in Bioinformatics and I bought this book to help me learn Perl for my job. During my training at the University, I wasn't taught Perl, because most programs... Read more
Published on July 15, 2011 by SB
5.0 out of 5 stars Easy to digest
I bought this book to create a working knowledge of programming, especially in the light of bioinformatics (I'm a biology grad student). Read more
Published on November 8, 2010 by maneki neko
3.0 out of 5 stars Not really for beginners!
It seems to be a very good book, but not basic at all! You need to know a lot of perl language before using this book.
Published on September 11, 2010 by D.R.
5.0 out of 5 stars I loved this book:
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... Read more
Published on January 7, 2010 by John Knepper
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