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Author Tisdall, James D.

Title Beginning Perl for bioinformatics / James D. Tisdall. [O'Reilly electronic resource]

Edition 1st ed.
Imprint Beijing ; Sebastopol, CA : O'Reilly, ©2001.
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Description 1 online resource (xiii, 368 pages) : illustrations
text file
Bibliography Includes bibliographical references (pages 309-314) and index.
Note "An introduction to Perl for biologists"--Cover
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.
Access Use copy Restrictions unspecified star MiAaHDL
Reproduction Electronic reproduction. [Place of publication not identified] : HathiTrust Digital Library, 2010. MiAaHDL
System Details 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
Processing Action digitized 2010 HathiTrust Digital Library committed to preserve pda MiAaHDL
Language English.
Subject Perl (Computer program language)
Bioinformatics.
Computational biology.
Computational Biology
Perl (Langage de programmation)
Bio-informatique.
Computational biology
Bioinformatics
Perl (Computer program language)
PERL.
Bio-informatica.
Indexed Term bioinformatics
Bioinformatics
Gegevensverwerking, databasebeheer
Bioinformatica (algemeen)
Data Processing, Database Management
Bioinformatics (General)
programming languages
programmeertalen
textbooks
studieboeken
genetic code
genetische code
gene expression
genexpressie
dna sequencing
nucleotide sequences
nucleotidenvolgordes
programming
programmeren
data analysis
gegevensanalyse
Genre Electronic book.
Other Form: Print version: Tisdall, James D. Beginning Perl for bioinformatics. 1st ed. Beijing ; Sebastopol, CA : O'Reilly, ©2001 0596000804 (DLC) 2002277715 (OCoLC)49583667
ISBN 9780596516277 (electronic bk.)
0596516274 (electronic bk.)
9780596550479 (electronic bk.)
0596550472 (electronic bk.)
Standard No. 0596000804
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