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Tables of Contents for Beginning Perl for Bioinformatics
Chapter/Section Title
Page #
Page Count
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