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Beginning Perl for bioinformatics /
This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you'll finish the book with the skills to tackle more advanced bioinformatics progr...
| Clasificación: | Libro Electrónico |
|---|---|
| Autor principal: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Beijing ; Sebastopol, CA :
O'Reilly,
©2001.
|
| Edición: | 1st ed. |
| Temas: | |
| Acceso en línea: | Texto completo (Requiere registro previo con correo institucional) |
Tabla de Contenidos:
- 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.