Beginning Perl for bioinformatics

1. Biology and Computer Science 1 -- Organization of DNA 2 -- 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. Art of Programming 18 -- Individual Approaches to Programming 18 -- Edit--Run--Revise (and Save) 19 -- An Environment of Programs 21 -- Programming Strategies 22 -- 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 -- 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 -- 6. Subroutines and Bugs 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 -- 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 -- 8. Genetic Code 149 -- Hashes 149 -- Data Structures and Algorithms for Biology 150 -- Genetic Code 155 -- Translating DNA into Proteins 163 -- Reading DNA from Files in FASTA Format 166 -- Reading Frames 175 -- 9. Restriction Maps and Regular Expressions 182 -- Regular Expressions 182 -- Restriction Maps and Restriction Enzymes 184 -- Perl Operations 197 -- 10. GenBank 199 -- GenBank Files 200 -- GenBank Libraries 203 -- Separating Sequence and Annotation 205 -- Parsing Annotations 212 -- Indexing GenBank with DBM 232 -- 11. Protein Data Bank 238 -- Files and Folders 240 -- PDB Files 248 -- Parsing PDB Files 257 -- Controlling Other Programs 267 -- 12. BLAST 274 -- Obtaining BLAST 275 -- String Matching and Homology 276 -- BLAST Output Files 277 -- Parsing BLAST Output 280 -- Presenting Data 290 -- Bioperl 294 -- 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