Beginning Perl for Bioinformatics Book

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