| Description |
1 online resource (xiii, 368 pages) : illustrations |
| Contents |
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 |
| Summary |
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 programming |
| Analysis |
bioinformatics |
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Bioinformatics |
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Gegevensverwerking, databasebeheer |
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Bioinformatica (algemeen) |
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Data Processing, Database Management |
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Bioinformatics (General) |
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programming languages |
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programmeertalen |
|
textbooks |
|
studieboeken |
|
genetic code |
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genetische code |
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gene expression |
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genexpressie |
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dna sequencing |
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nucleotide sequences |
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nucleotidenvolgordes |
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programming |
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programmeren |
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data analysis |
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gegevensanalyse |
| Bibliography |
Includes bibliographical references (pages 309-314) and index |
| Notes |
"An introduction to Perl for biologists"--Cover |
|
Master and use copy. Digital master created according to Benchmark for Faithful Digital Reproductions of Monographs and Serials, Version 1. Digital Library Federation, December 2002. http://purl.oclc.org/DLF/benchrepro0212 MiAaHDL |
|
Copyright © O'Reilly Media, Incorporated 2001 |
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Copyright © O'Reilly Media, Inc. 2001 |
|
English |
|
Print version record |
|
digitized 2010 HathiTrust Digital Library committed to preserve pda MiAaHDL |
| Subject |
Perl (Computer program language)
|
|
Bioinformatics.
|
|
Computational biology.
|
|
Computational Biology
|
|
COMPUTERS -- Programming Languages -- C♯
|
|
COMPUTERS -- Programming Languages -- Java.
|
|
COMPUTERS -- Programming Languages -- Pascal.
|
|
Computational biology
|
|
Bioinformatics
|
|
Perl (Computer program language)
|
|
PERL.
|
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Bio-informatica.
|
| Genre/Form |
Electronic book
|
| Form |
Electronic book
|
| ISBN |
9780596516277 |
|
0596516274 |
|
9780596550479 |
|
0596550472 |
|
