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9780596000806

Beginning Perl for Bioinformatics

by
  • ISBN13:

    9780596000806

  • ISBN10:

    0596000804

  • Edition: 1st
  • Format: Paperback
  • Copyright: 2002-01-01
  • Publisher: Oreilly & Associates Inc

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Summary

Major advances like the Human Genome Project show that programming is becoming as central to the biological sciences as it has been to physics or astronomy. As the field of bioinformatics picks up speed, biologists are more and more eager to add programming ability to their laboratory toolkits, and Perl leads the field as the language of choice for biological data analysis. Beginning Perl for Bioinformatics is a practical introduction to biological programming using Perl, the most popular language for bioinformatic analysis. Perl is strong in precisely what is needed to analyze biological data: string handling, text processing, networking, ability to control other programs, and rapid prototyping. Using this book as a springboard, biologists with no previous programming skills will be able to get up to speed quickly and embark on successful programming projects.

Author Biography

James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.

Table of Contents

Preface vii
Biology and Computer Science
1(5)
The Organization of DNA
2(1)
The Organization of Proteins
3(1)
In Silico
4(1)
Limits to Computation
5(1)
Getting Started with Perl
6(12)
A Low and Long Learning Curve
6(2)
Perl's Benefits
8(2)
Installing Perl on Your Computer
10(3)
How to Run Perl Programs
13(2)
Text Editors
15(1)
Finding Help
16(2)
The Art of Programming
18(11)
Individual Approaches to Programming
18(1)
Edit---Run---Revise (and Save)
19(2)
An Environment of Programs
21(1)
Programming Strategies
22(1)
The Programming Process
23(6)
Sequences and Strings
29(27)
Representing Sequence Data
29(3)
A Program to Store a DNA Sequence
32(4)
Concatenating DNA Fragments
36(4)
Transcription: DNA to RNA
40(2)
Using the Perl Documentation
42(1)
Calculating the Reverse Complement in Perl
43(3)
Proteins, Files, and Arrays
46(1)
Reading Proteins in Files
47(3)
Arrays
50(4)
Scalar and List Context
54(1)
Exercises
55(1)
Motifs and Loops
56(31)
Flow Control
56(6)
Code Layout
62(1)
Finding Motifs
63(7)
Counting Nucleotides
70(1)
Exploding Strings into Arrays
71(6)
Operating on Strings
77(4)
Writing to Files
81(4)
Exercises
85(2)
Subroutines and Bugs
87(31)
Subroutines
87(3)
Scoping and Subroutines
90(6)
Command-Line Arguments and Arrays
96(2)
Passing Data to Subroutines
98(4)
Modules and Libraries of Subroutines
102(2)
Fixing Bugs in Your Code
104(12)
Exercises
116(2)
Mutations and Randomization
118(31)
Random Number Generators
119(1)
A Program Using Randomization
120(6)
A Program to Simulate DNA Mutation
126(10)
Generating Random DNA
136(5)
Analyzing DNA
141(6)
Exercises
147(2)
The Genetic Code
149(33)
Hashes
149(1)
Data Structures and Algorithms for Biology
150(5)
The Genetic Code
155(8)
Translating DNA into Proteins
163(3)
Reading DNA from Files in FASTA Format
166(9)
Reading Frames
175(5)
Exercises
180(2)
Restriction Maps and Regular Experssions
182(17)
Regular Expressions
182(2)
Restriction Maps and Restriction Enzymes
184(13)
Perl Operations
197(1)
Exercises
198(1)
GenBank
199(39)
GenBank Files
200(3)
GenBank Libraries
203(2)
Separating Sequence and Annotation
205(7)
Parsing Annotations
212(20)
Indexing GenBank with DBM
232(4)
Exercises
236(2)
Protein Data Bank
238(36)
Files and Folders
240(8)
PDB Files
248(9)
Parsing PDB Files
257(10)
Controlling Other Programs
267(5)
Exercises
272(2)
Blast
274(28)
Obtaining BLAST
275(1)
String Matching and Homology
276(1)
BLAST Output Files
277(3)
Parsing BLAST Output
280(10)
Presenting Data
290(4)
Bioperl
294(7)
Exercises
301(1)
Further Topics
302(5)
The Art of Program Design
302(1)
Web Programming
302(1)
Algorithms and Sequence Alignment
303(1)
Object-Oriented Programming
303(1)
Perl Modules
303(1)
Complex Data Structures
304(1)
Relational Databases
304(1)
Microarrays and XML
305(1)
Graphics Programming
305(1)
Modeling Networks
305(1)
DNA Computers
306(1)
Resources 307(8)
Perl Summary 315(32)
Index 347

Supplemental Materials

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The New copy of this book will include any supplemental materials advertised. Please check the title of the book to determine if it should include any access cards, study guides, lab manuals, CDs, etc.

The Used, Rental and eBook copies of this book are not guaranteed to include any supplemental materials. Typically, only the book itself is included. This is true even if the title states it includes any access cards, study guides, lab manuals, CDs, etc.

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