Beginning Perl for Bioinformatics

Free download Beginning Perl for Bioinformatics in PDF written by James Tisdall and published by O’Reilly Publishers.

According to the Author, “This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving particular problems or class of problems, so you’ll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to tackle more advanced bioinformatics programming.  

This book is a tutorial for biologists on how to program, and is designed for beginning programmers. The examples and exercises with only a few exceptions use biological data. The book’s goal is twofold: it teaches programming skills and applies them to interesting biological areas. I want to get you up and programming as quickly and painlessly as possible. I aim for simplicity of explanation, not completeness of coverage. I don’t always strictly define the programming concepts, because formal definitions can be distracting. The Perl language makes it possible to start writing real programs quickly. As you continue reading this book and the online Perl documentation, you’ll fill in the details, learn better ways of doing things, and improve your understanding of programming concepts. Depending on your style of learning, you can approach this material in different ways. One way, as the King gravely said to Alice, is to “Begin at the beginning and go on till you come to the end: then stop.” (This line from Alice in Wonderland is often used as a whimsical definition of an algorithm.) The material is organized to be read in this fashion, as a narrative.

Another approach is to get the programs into your computer, run them, see what they do, and perhaps try to alter this or that in the program to see what effect your changes have. This may be combined with a quick skim of the text of the chapter. This is a common approach used by programmers when learning a new language. Basically, you learn by imitation, looking at actual programs. Anyone wishing to learn Perl programming for bioinformatics should try the exercises found at the end of most chapters. They are given in approximate order of difficulty, and some of the higher-numbered exercises are fairly challenging and may be appropriate for classroom projects. Because there’s more than one way to do things in Perl, there is no one correct answer to an exercise. If you’re a beginning programmer, and you manage to solve an exercise in any way whatsoever, you’ve succeeded at that exercise.

Table of Content

  1. Biology and Computer Science
  2. Getting Started with Perl
  3. The Art of Programming
  4. Sequences and Strings
  5. Motifs and Loops
  6. Subroutines and Bugs
  7. Mutations and Randomization 
  8. The Genetic Code
  9. Restriction Maps and Regular Expressions
  10. GenBank
  11. Protein Data Bank
  12. Blast
  13. Further Topics
  14. Resources
  15. Perl Summary

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