Perl for Exploring DNA [Paperback]

Mark D. LeBlanc (Author), Betsey Dexter Dyer (Author)

Book Description

Publication Date: August 10, 2007

This book presents Perl programming with a uniquely interdisciplinary perspective for the bioinformatics classroom. The co-authors are a professor of computer science and a professor of biology who collaborate in developing software for DNA sequence analysis. A specialty of the authors is encouraging interdisciplinary undergraduate research. The book has been tested in the classroom as a text for both biology and computer science majors. Benefiting from years of teaching experience in both computer science and biology, the authors use an exceptionally friendly and pedagogically sound introduction to Perl that emphasizes good programming practices throughout. Concepts include a rich introduction to working with strings and files of sequence data, control structures, subroutines, and data structures (e.g., arrays and hash tables). A particularly unique feature of the text is the early and repeated exposure to and use of regular expressions in sequence analysis. All examples in the book are applied to biological sequence analysis (DNA analysis, Protein analysis). The full-length book is appropriate for majors in either computer science or biology and especially relevant for new interdisciplinary courses involving students from multiple disciplines.

Editorial Reviews

About the Author

Mark D. Leblanc is Professor of Computer Science and Betsey Dexter Dyer is Professor of Biology, both at Wheaton College, Massachusetts.

Product Details

• Paperback: 288 pages
• Publisher: Oxford University Press, USA; First Edition edition (August 10, 2007)
• Language: English
• ISBN-10: 0195305892
• ISBN-13: 978-0195305890
• Product Dimensions: 9.9 x 7 x 0.7 inches
• Shipping Weight: 1 pounds (View shipping rates and policies)
• Average Customer Review: 3.6 out of 5 stars  See all reviews (8 customer reviews)
• Amazon Best Sellers Rank: #935,759 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

5 of 5 people found the following review helpful:

5.0 out of 5 stars great first perl book, January 3, 2010

By 

C. E. Wells (SC, United States) - See all my reviews
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This review is from: Perl for Exploring DNA (Paperback)

I really disagree with the negative reviews here. This is a GREAT book for the biologist who is making their first foray into perl programming. Maybe a professional programmer would take issue with presentation format -- but as a PhD. biologist with little programming experience - I can tell you that this has been a wonderful resource for me. I worked through the book cover to cover while simultaneously writing some programs for my own work. I feel very comfortable with the overall logic of the language now and ready to take on more complex texts.

In addition, the book is well-written and includes a great deal of interesting background on both molecular biology and programming. Frankly, if I were teaching a graduate course in this area I would not hesitate to take this as a textbook. The writing is clear and the progression of subjects logical. It would hold students' interest, certainly.

6 of 7 people found the following review helpful:

4.0 out of 5 stars Great beginner guide to Perl, September 5, 2007

By 

Teodor Zlatanov "Теод... (USA) - See all my reviews
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This review is from: Perl for Exploring DNA (Paperback)

"Perl for Exploring DNA" should have been named "Beginner Perl for Exploring DNA" instead. That sums up the scope and level of detail in the book. I think as a compromise between teaching Perl and using Perl for DNA analysis it succeeds. In fact I would recommend it to beginner Perl programmers interested in text analysis over most other beginner Perl books in the market. Complex data structures are explained well, though late in the book.

I can appreciate the formidable task of trying to present Perl to biologists. There are many ideas and techniques that come naturally to someone trained in computer science or engineering, but which are arcane or counter-intuitive to everyone else. Something like CPAN, to address a previous review of the book which mentioned that CPAN was not prominent enough, seems painfully necessary to a programmer but requires a good understanding of many aspects of Perl (including the CPAN shell). It's not easy to present these concepts, especially if the audience is biologists who are more worried about that experiment they left running overnight than how to force install a CPAN module.

I found the sidebars interesting, the code examples understandable, and the book well written. I think there are particular tasks in text analysis that this book addresses very well in its pursuit of DNA-oriented Perl training. As a general guide it's only part of the necessary material, but I wouldn't hesitate to recommend it.

5 of 6 people found the following review helpful:

5.0 out of 5 stars Excellent interdisciplinary text for bioinformatics, September 1, 2008

By 

Marc L. Smith (Poughkeepsie, NY USA) - See all my reviews
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This review is from: Perl for Exploring DNA (Paperback)

I used Perl for Exploring DNA (PEDNA) for an undergraduate course in Bioinformatics last spring, and have adopted it once again for this fall. Our course is cross-listed and co-taught by our college's CS and Biology departments, and students who register come from the same variety of backgrounds. I searched for a long time to find an appropriate text to support the CS content in the course, and despite my initial reluctance to use Perl (my preferences would have been more for Ruby or Python), on the strength of the PEDNA approach adopted this text. Things worked out very well, and I couldn't be happier with the results.

Why PEDNA, then? The truth is, the language doesn't matter as long as it supports the goal of teaching computer science and biology students to speak each other's language and participate mutually in the process of problem solving and algorithm design. A text that assumes the reader has a programming background can be intimidating to a reader who does not, and this was my concern with most Perl texts I surveyed. Similarly, a text gentle enough for programming novices that teaches Perl tends not to possess the desired bioinformatics content for our course, and runs the risk of losing the interest of its readers with a computer science background.

Amid this despair of self-inflicted and conflicting goals for our course, and just in time before the semester began, the PEDNA text was published. After quickly reading this book from cover to cover, I realized it was almost perfect for my needs--I say *almost* because it uses Perl, but I've since come to terms with this choice, primarily on the strength of the Perl presentation, and only secondarily on the wide-spread adoption of Perl in the bioinformatics community. PEDNA focuses upfront on strings, regular expressions and the desire for biologists to find patterns in DNA data, but uses pattern-matching for words in an English dictionary as an analogy to bring non-biologists on board.

Throughout the text, Perl is introduced in the context of the history of biology, including important people, the questions they asked, the problems they worked on, and their solutions. While students are writing their first programs, the emphasis isn't on Perl but on the problem being solved. Information about the greater Perl community, and wisdom from Larry Wall is provided, but a discussion of the choice of language makes it clear that what the reader learns in PEDNA is readily applied to other programming languages.

What is marvelous about PEDNA is it's presentation of regex syntax and semantics using the transliteration (tr), substitution(s), and match (m) operators. Uniquely, Regex is presented and emphasized from the very beginning in PEDNA, and I can affirm from its use in the classroom, successfully. Searches and string manipulations that can't be tackled with these operators alone motivate the introduction of other Perl language features, including assignment statements, conditional execution, and loops. The authors throughout advocate and demonstrate a lovely, well-documented coding style. Later, subroutines, arrays, and hashes are introduced, at a point when these more sophisticated programming abstractions might be better understood by novice programmers. Most of the wonderful shortcuts and tricks Perl is noted for are not readily accessible to novices, and they are not included in PEDNA. Likewise, the decision was made to present one way, and not many ways to solve the problems presented.

This book alone will not turn the reader (especially not a Biologist) into an expert Perl programmer in its 276 pages, nor does it claim to do so. But in its brevity PEDNA keeps its promise, introducing its diverse intended audience to Using Perl for Exploring DNA. For those whom this book excites and who want more, references are provided, along with the encouragement to continue collaborating across disciplines to ask and answer questions about DNA.