Beginning Perl for Bioinformatics | 
 enlarge | Author: James Tisdall
Publisher: O'Reilly Media, Inc.
Category: Book
List Price: $39.95
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Avg. Customer Rating:  25 reviews
Sales Rank: 145637
Format: Illustrated
Media: Paperback
Edition: 1
Number Of Items: 1
Pages: 400
Shipping Weight (lbs): 1.4
Dimensions (in): 9.1 x 7 x 0.9
ISBN: 0596000804
Dewey Decimal Number: 005.133
UPC: 636920000808
EAN: 9780596000806
ASIN: 0596000804
Publication Date: October 15, 2001
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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
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.
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| Customer Reviews: Read 20 more reviews...
 A practical introduction to programming for biologists December 31, 2006
3 out of 3 found this review helpful
Although this book was written for biologists with no previous programming experience who have decided they need to learn to program in PERL, it is also useful for programmers entering the field of bioinformatics who need to learn the language. However, you should have some background in biology or else you'll be lost as to the purpose of the examples. That's because almost all of the examples and exercises are based on real biological problems, and this book will give you a good introduction to the most common bioinformatics programming problems and the most common computer-based biological data. This book is over five years old, but it still stands alone in that what it does it does better than any other book I've run across. The follow-on to this book is "Mastering Perl for Bioinformatics", and I recommend that book for both CS and biologist types that want to get into the more advanced parts of PERL and yet stay in the realm of learning the language via real biological problems. The following is a short run down of each chapter:
1. Biology and Computer Science - Covers some key concepts in molecular biology, as well as how biology and computer science fit together.
2. Getting Started with Perl - Shows you how to get Perl running on your computer and also talks about Perl's benefits.
3. The Art of Programming - Provides an overview as to how programmers accomplish their jobs. Some of the most important practical strategies good programmers use are explained, and where to find answers to questions that arise while you are programming is carefully laid out. These ideas are made concrete by brief narrative case studies that show how programmers, given a problem, find its solution.
4. Sequences and Strings - You start writing Perl programs with DNA and proteins. The programs transcribe DNA to RNA, concatenate sequences, make the reverse complement of DNA, and read sequence data from files. This is the first chapter to conclude with exercises.
5. Motifs and Loops - Continues demonstrating the basics of the Perl language with programs that search for motifs in DNA or protein, interact with users at the keyboard, write data to files, use loops and conditional tests, use regular expressions, and operate on strings and arrays.
6. Subroutines and Bugs -Extends the basic knowledge of Perl in two main directions: subroutines, which are an important way to structure programs, and the use of the Perl debugger, which can examine in detail a running Perl program.
7. Mutations and Randomizations - Genetic mutations, fundamental to biology, are modelled as random events using the random number generator in Perl. This chapter uses random numbers to generate DNA sequence data sets, and to repeatedly mutate DNA sequence. Loops, subroutines, and lexical scoping are also discussed.
8. The Genetic Code - How to translate DNA to proteins, using the genetic code. It also covers a good bit more of the Perl programming language, such as the hash data type, sorted and unsorted arrays, binary search, relational databases, and DBM, and how to handle FASTA formatted sequence data.
9. Restriction Maps and Regular Expressions - An introduction to Perl regular expressions. The main focus of the chapter is the development of a program to calculate a restriction map for a DNA sequence.
10. GenBank - The Genetic Sequence Data Bank (GenBank) is central to modern biology and bioinformatics. In this chapter, you learn how to write programs to extract information from GenBank files and libraries. You will also make a database to create your own rapid access lookups on a GenBank library.
11. Protein Data Bank - Develops a program that can parse Protein Data Bank (PDB) files. Some interesting Perl techniques are encountered while doing so, such as finding and iterating over lots of files and controlling other bioinformatics programs from a Perl program.
12. BLAST - Develops some code to parse a BLAST output file. Also mentioned are the Bioperl project and its BLAST parser, and some additional ways to format output in Perl.
13. Further Topics - Looks at topics beyond the scope of this book. These topics include sequence alignment methods like the Smith-Waterman algorithm and microarray techniques that enable the measurement of the relative levels of thousands of gene transcripts at a time. These topics are only briefly mentioned, and you are shown places outside of the book to get further information.
Appendix A - Resources for Perl and for bioinformatics programming, such as books and Internet sites.
Appendix B - Summary of those parts of the Perl language that will be most useful as you read this book.
 Reasonable book for learning Perl November 11, 2006
1 out of 1 found this review helpful
For the students of molecular biology and genetics, and also other bioinformatics-related departments, this book is an above-average supply to study Perl.
Mostly for the Biologist September 20, 2006
2 out of 2 found this review helpful
People come to Bioinformatics from either the bio side or the CS side, with a few from various other disciplines. This book is best for the bio person who is getting into programming, not the programmer who is getting into bio.
For you CS types, I attended a tutorial by Tisdall on this material some years ago. One of the attendees asked why you needed an editor to code in Perl. That is the level that we are dealing with here!
It is a crime that biology and biochem students are not taught any perl- this is a very useful tool that will be more important as time goes on.
Perhaps someone could write a book on bioinformatics Perl for programmers someday, but that is not the goal of this book.
Beginning Perl for BioInformatics January 16, 2006
2 out of 2 found this review helpful
Excellent book. The perl programming language is the most versitile and powerful software tool available today. This book was written for Biologists to learn this incredible programming language. Examples are pulled from real problems Biologists face and explained in terms they can understand. The book is clearly written.
excellent introduction... December 30, 2005
1 out of 1 found this review helpful
i find this book is an excellent intoudction for one of the most intersting topic..The book is so easy to read if you know the elementary of molecular biology and begining introudction about perl. I do recommed this book to start with if you interested about programming for bioinformatics. You will be able to build simple bioinformatics programmes after reading this book as well as you will be able to understand easily how the commerically avaliable bioinformatics programs are working.
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