Beginning Perl for bioinformatics: [an introduction to Perl for biologists]
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Beijing [u.a.]
O'Reilly
2001
|
| Ausgabe: | 1. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIII, 368 S. |
| ISBN: | 0596000804 |
Internformat
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Datensatz im Suchindex
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| adam_text | Titel: Beginning Perl for bioinformatics
Autor: Tisdall, James D.
Jahr: 2001
Table of Contents
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
Hi
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
Table of Contents
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
Table of Contents | v
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
Table of Contents
|
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| dewey-hundreds | 000 - Computer science, information, general works |
| dewey-ones | 005 - Computer programming, programs, data, security |
| dewey-raw | 005.133 |
| dewey-search | 005.133 |
| dewey-sort | 15.133 |
| dewey-tens | 000 - Computer science, information, general works |
| discipline | Biologie Informatik Chemie-Ingenieurwesen Biotechnologie |
| edition | 1. ed. |
| format | Book |
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| indexdate | 2024-07-09T18:54:49Z |
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| isbn | 0596000804 |
| language | English |
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| spelling | Tisdall, James D. Verfasser aut Beginning Perl for bioinformatics [an introduction to Perl for biologists] James D. Tisdall 1. ed. Beijing [u.a.] O'Reilly 2001 XIII, 368 S. txt rdacontent n rdamedia nc rdacarrier Bioinformatik - Programmierung - Perl <Programmiersprache> Perl Programmiersprache (DE-588)4307836-9 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Programmierung (DE-588)4076370-5 gnd rswk-swf Bioinformatik (DE-588)4611085-9 s Programmierung (DE-588)4076370-5 s Perl Programmiersprache (DE-588)4307836-9 s DE-604 Paralle Sprachausgabe deutsch Tisdall, James D. Einführung in Perl für Bioinformatik HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009540663&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Tisdall, James D. Beginning Perl for bioinformatics [an introduction to Perl for biologists] Bioinformatik - Programmierung - Perl <Programmiersprache> Perl Programmiersprache (DE-588)4307836-9 gnd Bioinformatik (DE-588)4611085-9 gnd Programmierung (DE-588)4076370-5 gnd |
| subject_GND | (DE-588)4307836-9 (DE-588)4611085-9 (DE-588)4076370-5 |
| title | Beginning Perl for bioinformatics [an introduction to Perl for biologists] |
| title_auth | Beginning Perl for bioinformatics [an introduction to Perl for biologists] |
| title_exact_search | Beginning Perl for bioinformatics [an introduction to Perl for biologists] |
| title_full | Beginning Perl for bioinformatics [an introduction to Perl for biologists] James D. Tisdall |
| title_fullStr | Beginning Perl for bioinformatics [an introduction to Perl for biologists] James D. Tisdall |
| title_full_unstemmed | Beginning Perl for bioinformatics [an introduction to Perl for biologists] James D. Tisdall |
| title_short | Beginning Perl for bioinformatics |
| title_sort | beginning perl for bioinformatics an introduction to perl for biologists |
| title_sub | [an introduction to Perl for biologists] |
| topic | Bioinformatik - Programmierung - Perl <Programmiersprache> Perl Programmiersprache (DE-588)4307836-9 gnd Bioinformatik (DE-588)4611085-9 gnd Programmierung (DE-588)4076370-5 gnd |
| topic_facet | Bioinformatik - Programmierung - Perl <Programmiersprache> Perl Programmiersprache Bioinformatik Programmierung |
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