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Beginning Perl for Bioinformatics 1st Edition

4.4 out of 5 stars 46 customer reviews
ISBN-13: 063-6920000808
ISBN-10: 0596000804
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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
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Product Details

  • Paperback: 400 pages
  • Publisher: O'Reilly Media; 1 edition (November 1, 2001)
  • Language: English
  • ISBN-10: 0596000804
  • ISBN-13: 978-0596000806
  • Product Dimensions: 7 x 0.8 x 9.2 inches
  • Shipping Weight: 1.2 pounds (View shipping rates and policies)
  • Average Customer Review: 4.4 out of 5 stars  See all reviews (46 customer reviews)
  • Amazon Best Sellers Rank: #459,977 in Books (See Top 100 in Books)

Customer Reviews

Top Customer Reviews

By Dr. Lee D. Carlson HALL OF FAMEVINE VOICE on 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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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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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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