Beginning Perl for Bioinformatics
An Introduction to Perl for Biologists
Publisher: O'Reilly Media
Final Release Date: October 2001
Pages: 386

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
Table of Contents
Product Details
About the Author
Colophon
Recommended for You
Customer Reviews

REVIEW SNAPSHOT®

by PowerReviews
oreillyBeginning Perl for Bioinformatics
 
3.8

(based on 8 reviews)

Ratings Distribution

  • 5 Stars

     

    (0)

  • 4 Stars

     

    (6)

  • 3 Stars

     

    (2)

  • 2 Stars

     

    (0)

  • 1 Stars

     

    (0)

Reviewed by 8 customers

Sort by

Displaying reviews 1-8

Back to top

(3 of 3 customers found this review helpful)

 
4.0

Great tool for anyone getting into the field

By Alos Diallo

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

I used this book when I was a researcher in college and it helped a lot. Many of the examples in the book are directly applicable to work you will do in a lab. While this book does not have everything I found it an invaluable resource for anyone who is new to perl and bioinformatics in general.

(1 of 1 customers found this review helpful)

 
4.0

Beginning Perl for Bioinformatics Review

By Anonymous

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

this is the excellent online resource for the beginning programmers .

Only thing i like to mention is that should give more example on the bioinformatics codes...for different aspects.

Is there any resource for java like this one, which is specially made for bioinformatics using examples..

Please let me know.

(1 of 2 customers found this review helpful)

 
4.0

Beginning Perl for Bioinformatics Review

By yupeng cun

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

it gives me a programing world!

(0 of 1 customers found this review helpful)

 
4.0

Beginning Perl for Bioinformatics Review

By Kate Lea

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

This is good book, I ahvent read it all but its very comprehesive! I think that I'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank. Bye Kate Lea

(0 of 1 customers found this review helpful)

 
4.0

Beginning Perl for Bioinformatics Review

By Kate Lea

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

This is good book, I ahvent read it all but its very comprehesive! I think that I'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank. Bye Kate Lea

(2 of 2 customers found this review helpful)

 
4.0

Beginning Perl for Bioinformatics Review

By Seungwoo Hwang

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

This is certainly a superb book. I really enjoyed it. Here are some of the advantages of "Beginning Perl for Bioinformatics" over other entry level general purpose Perl books such as "Learning Perl".

(1) Most importantly, you learn Perl in the context of dealing with biological problems (e.g., parsing BLAST output) rather than general problems that will not even remotly interest you (e.g., parsing employee's address list). So you will be kept interested throughout the book.

(2) Entire codes, rather than code snippets, are presented.

(3) Explanations are much more friendly and clear.

(4) You can find some useful materials that are not covered in Learning Perl; for example, using Perl debugger, using range operator to skip lines, etc.

One problem with this book is that there are TONS of errata (I'm referring to October 2001, 1st edition). Most of their corrections are available from the book website, and half of them are re-phrasing of sentences, so errata will not prevent you from understanding the book. But it certainly takes significant amount of time to go through the HUGE list of errata corrections (I also found more than ten additional errata that are not found in the errata list and reported to publisher). So if it's not urgent for you, wait until next reprint becomes available.

One more wish list is that Bioperl module could have been covered (It is briefly mentioned over seven pages but not actually covered). Hopefully, the upcoming book (June 2003) "Mastering perl for bioinformatics" will cover it.

(1 of 1 customers found this review helpful)

 
3.0

Beginning Perl for Bioinformatics Review

By ed

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

it's a decent book -- but there needs to be one devoted to BioPerl!

(1 of 1 customers found this review helpful)

 
3.0

Beginning Perl for Bioinformatics Review

By Ken Nguyen

from Undisclosed

Comments about oreilly Beginning Perl for Bioinformatics:

This book is ok, not all that great for beginners. Has a lot of info, and the author shows you how to solve specific problems, but does not really show you how to deal with related problems. There are many errors, which is not unusual when people write books. The best way to learn perl is that you still have to learn the perl language itself to really understand it. This books has lots of examples, and if you happen to have the exact problems that you need to solve, then it is not bad. But to be honest with all you readers, the best way still is to read from other orielly's books on perl. And start programming from scratch! Goodluck to all ya!

Displaying reviews 1-8

Back to top

 
Buy 2 Get 1 Free Free Shipping Guarantee
Buying Options
Immediate Access - Go Digital what's this?
Ebook: $31.99
Formats:  DAISY, ePub, Mobi, PDF
Print & Ebook: $43.95
Print: $39.95