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Beginning Perl for Bioinformatics [Paperback]

James Tisdall
4.4 out of 5 stars  See all reviews (7 customer reviews)
Price: 30.99 & FREE Delivery in the UK. Details
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Book Description

1 Nov 2001 0596000804 978-0596000806 1

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

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Beginning Perl for Bioinformatics + Mastering Perl for Bioinformatics + Developing Bioinformatics Computer Skills
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Product details

  • Paperback: 386 pages
  • Publisher: O'Reilly Media; 1 edition (1 Nov 2001)
  • Language: English
  • ISBN-10: 0596000804
  • ISBN-13: 978-0596000806
  • Product Dimensions: 24.5 x 16.3 x 2.1 cm
  • Average Customer Review: 4.4 out of 5 stars  See all reviews (7 customer reviews)
  • Amazon Bestsellers Rank: 294,583 in Books (See Top 100 in Books)
  • See Complete Table of Contents

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Review

".....it is highly recommended for biologists and computer scientists who are new to the field of bioinformatics." -- Darryl Nishamura, Bioinformatics and Internet Report, Vol 3 Number 2, 2002

"Exactly what the average, over-worked geneticist needs." -- Gregory V. Wilson, Dr Dobbs Journal, June 2002

"James Tisdall's Beginning Perl for Bioinformatics, on the other hand, is exactly what the average over-worked geneticist needs....." -- Greg V. Wilson, Dr Dobbs, June 2002

Good for biotech professionals who are familiar with bio concepts and need to brush up on the practical computer science aspects of their field. -- Netsurfer Digest, Jan 2002

It's a solid book, and one that should be able to get people learning Perl, genetics, or both up to speed and working on real world problems quickly. -- Babbage, slashdot.org, Jan 2002

Book Description

An Introduction to Perl for Biologists

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Customer Reviews

4.4 out of 5 stars
4.4 out of 5 stars
Most Helpful Customer Reviews
17 of 17 people found the following review helpful
By A Customer
Format:Paperback
I found this book excellent, it contains the solution to most programmes required for bioinformatics and creating a web-site. I mean as a biologist with no experience in computer programming i was scared when it came to programme using perl but this book is literally a god-send and provided most of the solutions to build biological web-sites from finding pattern matching restriction sites in a nucleotide sequence to extracting specific information from sequences and transforming nucleotide sequences into amino acid sequences and building web pages from it.
You have to buy this book if you are new to the world of perl or bioinformatics.
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10 of 11 people found the following review helpful
Format:Paperback
I think this is a really good introduction to both Perl and Bioinformatics programming. I already know several other languages, and have been meaning to pick up Perl for a while. So I thought this book might be too basic for me, but because I was new to the field of Bioinformatics, I did not find it terribly basic. I also do believe that it would be very good for someone with a biology background wanting to learn perl for bioinformatics (this is the audience the book claims to be targeting). Perl is a very powerful language, and I do think that it could be hard for programming beginner to learn. However, I think this book does a very good job of introducing several important topics in Perl gently. The best thing about it is the extremely numerous examples, which can all be downloaded from the book's website, so you don't have to waste time typing them in. This provides a great source of learning and experimenting with the code, but it also provides a platform for developing more advanced programs. You can just build new programs on top of much of the code from the book, which is very convenient, and is also what programming efficiently is all about.
There are 13 chapters in the book, and I'll give a quick summary and insight into each below:
Chapter 1 Biology and computer science: This gives a quick and gentle introduction to the goals of the field of bioinformatics, and how the two fields of biology and computer science contribute to it. It sets the context of the book.
Chapter 2 Getting started with Perl: This is a good chapter which details how to set up Perl on your computer, and get started using it.
Chapter 3 The art of programming: This chapter discusses the common approaches that people take to programming, and open source programming.
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7 of 8 people found the following review helpful
2.0 out of 5 stars Not far from Awful... 21 Oct 2003
Format:Paperback
I was advised to buy this book by my supervisor when I started my PhD in Bioinformatics. I had no previous programing experience and I was told that perl was the best way forward. It turned out perl was the best way forward, but not using this book. Perl is a very simple and intuitive language which a joy to work with.
This book tackles biological problems but with a poor approach. It forces you to copy down pages of code to form your first programs, and barely explains why you are doing it. What happens is that you miss out a word or spell something wrong and your program doesn't work, you get annoyed, you smash something! In contrast, the world renouned "learning perl" book teaches you why you do things and you build up your perl from a solid base. Yes this book focuses on the problem of using perl for biological problems, but that really isn't necessary. What you need is to learn the programming language, then when you are sure you know enough, you can apply it to your own problems. A solve them easily.
Buy "learning perl, O'reilly press" and then proceed to "programming perl, O'reilly press", there are far better books and will give you a solid grounding to tackle bioinformatics problems.
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1 of 1 people found the following review helpful
5.0 out of 5 stars Good to go. 4 Dec 2004
Format:Paperback
I'm one of those people who should be doing something better! But since this book is good, because my copy is bent to pieces, I thought I would offer up my vote for a good read.
clear follow through, gives you coded programs - not just snipits! that don't work on there own. Lets you cut the bits out you don't need etc... up to speed fast with the little bit of code you needed. No point learning everthing perl can do! only to chop some sequences etc... otherwise you wouldn't be buying this book, you'd buy a specific perl book
fun read too, with websites you might not yet know about.
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