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Genomic Perl: From Bioinformatics Basics to Working Code [Hardcover]

Rex A. Dwyer
3.7 out of 5 stars  See all reviews (3 customer reviews)
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Book Description

Dec 16 2002 052180177X 978-0521801775 1
In this introduction to computational molecular biology, Rex Dwyer explains many basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, he covers the biological background for each problem, develops a model for the solution, and then introduces the Perl concepts needed to implement the solution. The chapters discuss pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. Concrete examples and a step-by-step approach enable readers to grasp the computational and statistical methods.

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Review

"I found this to be an excellent book, and would not hesitate to recommend it to advanced undergraduate and postgraduate students."
Saturnino Luz, Computing Reviews


"[Those] with an adequate knowledge of bioinformatics may benefit from this book since the accompanying Perl source code can be easily extended and deployed... The structure of each chapter [is] simple and easy to follow."
Raymond Wan, University of Melbourne for SIGACT News

Book Description

This textbook explains how to write Perl computer programs to process the DNA data and other kinds of data coming from the Human Genome Project and similar sources. With minimal prerequisites, the author explains the biological background for many of the basic computational problems arising in molecular biology, develops models for their solution, then introduces the Perl concepts needed to implement those solutions. Computer programmers and biologists alike can use this book to prepare themselves to work in this exciting field.

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3.7 out of 5 stars
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Most helpful customer reviews
1.0 out of 5 stars Not a good perl programming book period! Dec 17 2003
By A Customer
Format:Hardcover
This books tries to combine and explain both bioinformatics and perl programming yet fails miserably at both. Though I have taken a class on learning perl this code is difficult to read and poorly explained. The bioinformatics is useless because the examples are simply stupid. For example instead of using free energy to determine RNA folding the author uses hydrogen bonding which is completely irrelavent or predicting species by using %gc or %at content between two organsims also useless. If you are looking for bioinformatics programming tips this book will not help you.
Variables are introduced that are not explained and the program is written in the most condensed possible way making it difficult to read and leaving you wading through each line. I am thankful I have taken programming perl and bioinformatics or this book would be of zero value. If I could I would give this book a -5 stars. Check it out at a library before you BUY!!!!!!! Even if perl.com reviews the book favorably the biology is at best completely WRONG!!! Buy O'Riely's advanced bioinformatics.
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Format:Hardcover
Combines intuitive derivations of most key algorithms, thoughtful use of key references to illustrate solutions of main problems with a detailed example, and develop well documented, carefully programmed,perl toolkit. The 65 routines on the CD in UNIX, Windows, and Mac formats perform most of the essential maipulations of GenBank sequences. I only miss Hidden Markov Model routines.
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5.0 out of 5 stars a nice book Jan. 22 2004
By A Customer
Format:Hardcover
This book was very favorably reviewed on perl.com.
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Most Helpful Customer Reviews on Amazon.com (beta)
Amazon.com: 3.7 out of 5 stars  3 reviews
16 of 20 people found the following review helpful
1.0 out of 5 stars Not a good perl programming book period! Dec 17 2003
By A Customer - Published on Amazon.com
Format:Hardcover
This books tries to combine and explain both bioinformatics and perl programming yet fails miserably at both. Though I have taken a class on learning perl this code is difficult to read and poorly explained. The bioinformatics is useless because the examples are simply stupid. For example instead of using free energy to determine RNA folding the author uses hydrogen bonding which is completely irrelavent or predicting species by using %gc or %at content between two organsims also useless. If you are looking for bioinformatics programming tips this book will not help you.
Variables are introduced that are not explained and the program is written in the most condensed possible way making it difficult to read and leaving you wading through each line. I am thankful I have taken programming perl and bioinformatics or this book would be of zero value. If I could I would give this book a -5 stars. Check it out at a library before you BUY!!!!!!! Even if perl.com reviews the book favorably the biology is at best completely WRONG!!! Buy O'Riely's advanced bioinformatics.
5.0 out of 5 stars Five Stars July 1 2014
By Anup B. - Published on Amazon.com
Verified Purchase
Good book with codes
6 of 12 people found the following review helpful
5.0 out of 5 stars Develops effective genomic toolkits for UNIX, Windows & Mac March 22 2003
By Amazon Customer - Published on Amazon.com
Format:Hardcover|Verified Purchase
Combines intuitive derivations of most key algorithms, thoughtful use of key references to illustrate solutions of main problems with a detailed example, and develop well documented, carefully programmed,perl toolkit. The 65 routines on the CD in UNIX, Windows, and Mac formats perform most of the essential maipulations of GenBank sequences. I only miss Hidden Markov Model routines.
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