Beginning Perl for bioinformatics / James D. Tisdall.

Format:

Book

Author/Creator:

Tisdall, James D.

Language:

English

Subjects (All):

Bioinformatics.

Perl (Computer program language).

Physical Description:

1 online resource (386 p.)

Edition:

First edition.

Place of Publication:

Sebastopol, California : O'Reilly, 2001.

Language Note:

English

System Details:

text file

Summary:

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 q

Contents:

Table of Contents; Preface; What Is Bioinformatics?; What Bioinformatics Can Do; About This Book; Who This Book Is For; Why Should I Learn to Program?; Structure of This Book; Conventions Used in This Book; Comments and Questions; Acknowledgments; Chapter 1. Biology and Computer Science; The Organization of DNA; The Organization of Proteins; In Silico; Limits to Computation; Chapter 2. Getting Started with Perl; A Low and Long Learning Curve; Perl's Benefits; Ease of Programming; Rapid Prototyping; Portability, Speed, and Program Maintenance; Versions of Perl; Installing Perl on Your Computer

Perl May Already Be Installed!No Internet Access?; Downloading; Binary Versus Source Code; Installation; Unix and Linux; Macintosh; Windows; How to Run Perl Programs; Unix or Linux; Macs; Windows; Text Editors; Finding Help; Chapter 3. The Art of Programming; Individual Approaches to Programming; Edit-Run-Revise (and Save); Saves and Backups; Error Messages; Debugging; An Environment of Programs; Open Source Programs; Programming Strategies; The Programming Process; The Design Phase; Algorithms; Pseudocode and Code; Comments; Chapter 4. Sequences and Strings; Representing Sequence Data

A Program to Store a DNA SequenceControl Flow; Comments Revisited; Command Interpretation; Statements; Variables; Strings; Assignment; Print; Exit; Concatenating DNA Fragments; Transcription: DNA to RNA; Using the Perl Documentation; Calculating the Reverse Complement in Perl; Proteins, Files, and Arrays; Reading Proteins in Files; Arrays; Scalar and List Context; Exercises; Chapter 5. Motifs and Loops; Flow Control; Conditional Statements; Conditional tests and matching braces; Loops; open and unless; Code Layout; Finding Motifs; Getting User Input from the Keyboard

Turning Arrays into Scalars with joindo-until Loops; Regular Expressions; Regular expressions and character classes; Pattern matching with =~ and regular expressions; Counting Nucleotides; Exploding Strings into Arrays; Operating on Strings; Writing to Files; Exercises; Chapter 6. Subroutines and Bugs; Subroutines; Advantages of Subroutines; Writing Subroutines; Scoping and Subroutines; Arguments; Scoping; Command-Line Arguments and Arrays; Passing Data to Subroutines; Subroutines: Pass by Reference; Modules and Libraries of Subroutines; Fixing Bugs in Your Code; use warnings; and use strict

Fixing Bugs with Comments and Print Statements; The Perl Debugger; A program with bugs; How to start and stop the debugger; Debugger command summary; Stepping through statements with the debugger; Setting breakpoints; Fixing another bug; use warnings; and use strict; redux; Exercises; Chapter 7. Mutations and Randomization; Random Number Generators; A Program Using Randomization; Seeding the Random Number Generator; Control Flow; Making a Sentence; Randomly Selecting an Element of an Array; Formatting; Another Way to Calculate the Random Position; A Program to Simulate DNA Mutation

Pseudocode Design

Notes:

"An introduction to Perl for biologists"--Cover.

Includes bibliographical references (pages 309-314) and index.

Description based on print version record.

ISBN:

9780596550479

0596550472

9780596516277

0596516274