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

Amazon.com® Reader Reviews (Ranked by Helpfulness)

Average Amazon.com® Rating:  Based on 29 Ratings

A practical introduction to programming for biologists - 2006-12-31
Reviewer Rating:
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.

I loved this book: - 2010-01-07
Reviewer Rating:
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 next internship. I was clueless to perl, and programming for that matter, when I got this book a long time ago. I painfully flipped each page from front to back, because it 'is' a technical book, and absorbed everything as much as possible. This book set me off in a direction that I never imagined. Although we're on the brink of version six of the language, this book will do you right in any aspect of computer programming. For a 'beginner' looking to get into any language, this book is for you. It's painful, but try and take the time to really learn the information the book presents. It not only teaches you perl, but gives you a peek into the numerous databases and resources that exist as well as a terrific job of teaching you how to use regular expressions.

In the end, you'll have the foundation to become whatever kind of perl programmer you desire. If you're looking into bioinformatics, or a bioinformatician looking to learn, I recommend this book as well as 'Programming Perl', 'Mastering Perl for Bioinformatics', and 'BLAST'. 'BLAST' is fairly easy to breeze through and does a good job of explaining everything you would need to know. 'Mastering Perl...' picks up where this book left off, and 'Programming Perl' is one of the best buys I ever made, in regards to perl. I know these are all O REILLY books, but they're probably the best source for perl books out there. I'm not pitching their books either. Lastly, if you have the time I recommend you crunch on through 'CGI Programming with Perl'. Although the book is a bit out of date, it's definitely another 'piece' of the puzzle for someone to become a LAMP programmer.

good book for biologists - 2009-12-15
Reviewer Rating:
Very good book in perl for those biologist trying to merge their career into bioinformatics.

Beginning Perl is an excellent book. - 2009-09-08
Reviewer Rating:
Beginning Perl for Bioinformatics is an excellent, well-written text for the non-specialist person who wishes to program in perl. Although perl is indeed very powerful some concepts are rather unique and difficult to grasp if one understands other scripting languages. For a beginner, the book provides the necessary detail as required so as to progress rapidly. I would recommend it highly.

Great for Biologist that Don't Know How to Program - 2009-03-03
Reviewer Rating:
If you know anything about how to program then this book is NOT for you. This book is more geared towards biologists that know nothing about programming. If you fall in this category I recommend this book for you. Seriously, buy it and learn how to program so you can stop bugging people with better things to do to parse your BLAST output and FASTA files for you. In this day and age there is no reason why a biologist shouldn't have basic scripting abilities.

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