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Bioinformatics, biocomputing and Perl : an introduction to bioinformatics computing skills and practice / Michael Moorhouse, Paul Barry.
LIBRA QH324.2 .M667 2004
Available from offsite location
- Format:
- Book
- Author/Creator:
- Moorhouse, Michael (Michael John)
- Language:
- English
- Subjects (All):
- Bioinformatics.
- Computational biology.
- Perl (Computer program language).
- Physical Description:
- xix, 485 pages : illustrations ; 24 cm
- Place of Publication:
- Chichester ; Hoboken, NJ : Wiley, [2004]
- Summary:
- Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today's bioinformaticians.
- Contents:
- 1 Setting the Biological Scene 1
- 1.1 Introducing Biological Sequence Analysis 1
- 1.2 Protein and Polypeptides 4
- 1.3 Generalised Models and their Use 5
- 1.4 The Central Dogma of Molecular Biology 6
- 1.5 Genome Sequencing 10
- 1.6 The Example DNA-gene-protein system we will use 12
- 2 Setting the Technological Scene 15
- 2.1 The Layers of Technology 15
- 2.2 Finding per 17
- I Working with Perl 19
- 3.4 Selection 34
- 3.5 There Really is MTOWTDI 36
- 3.6 Processing Data Files 41
- 3.7 Introducing Patterns 44
- 4 Places to Put Things 49
- 4.1 Beyond Scalars 49
- 4.2 Arrays: Associating Data with Numbers 49
- 4.3 Hashes: Associating Data with Words 60
- 5 Getting Organised 71
- 5.1 Named Blocks 71
- 5.2 Introducing Subroutines 73
- 5.3 Creating Subroutines 74
- 5.4 Visibility and Scope 85
- 5.5 In-built Subroutines 90
- 5.6 Grouping and Reusing Subroutines 92
- 5.7 The Standard Modules 96
- 5.8 CPAN: The Module Repository 96
- 6 About Files 103
- 6.1 I/O: Input and Output 103
- 6.2 Reading Files 105
- 6.3 Writing Files 116
- 6.4 Chopping and Chomping 118
- 7 Patterns, Patterns and More Patterns 121
- 7.2 Introducing the Pattern Metacharacters 124
- 7.3 Anchors 132
- 7.4 The Binding Operators 134
- 7.5 Remembering What Was Matched 135
- 7.6 Greedy by Default 137
- 7.7 Alternative Pattern Delimiters 138
- 7.8 Another Useful Utility 139
- 7.9 Substitutions: Search and Replace 140
- 7.10 Finding a Sequence 142
- 8 Perl Grabbag 147
- 8.2 Strictness 147
- 8.3 Perl One-liners 149
- 8.4 Running Other Programs from per 152
- 8.5 Recovering from Errors 153
- 8.6 Sorting 155
- 8.7 HERE Documents 159
- The Maxims Repeated 161
- II Working with Data 163
- 9 Downloading Datasets 165
- 9.1 Let's Get Data 165
- 9.2 Downloading from the Web 165
- 10 The Protein Databank 173
- 10.2 Determining Biomolecule Structures 174
- 10.3 The Protein Databank 177
- 10.4 The PDB Data-file Formats 179
- 10.5 Accessing Data in PDB Entries 182
- 10.6 Accessing PDB Annotation Data 183
- 10.7 Contact Maps 192
- 10.8 STRIDE: Secondary Structure Assignment 196
- 10.9 Assigning Secondary Structures 197
- 10.10 Introducing the mmCIF Protein Format 205
- 11 Non-redundant Datasets 211
- 11.1 Introducing Non-redundant Datasets 211
- 11.2 Non-redundant Protein Structures 213
- The Maxims Repeated 217
- 12 Databases 219
- 12.1 Introducing Databases 219
- 12.2 Available Database Systems 224
- 12.3 SQL: the Language of Databases 226
- 12.4 A Database Case Study: MER 227
- 13 Databases and Perl 273
- 13.1 Why Program Databases? 273
- 13.2 Perl Database Technologies 274
- 13.3 Preparing Perl 275
- 13.4 Programming Databases with DBI 276
- 13.5 Customising Output 282
- 13.6 Customising Input 285
- 13.7 Extending SQL 289
- III Working with the Web 295
- 14 The Sequence Retrieval System 297
- 14.1 An Example of What's Possible 297
- 14.2 Why SRS? 298
- 14.3 Using SRS 298
- 15 Web Technologies 303
- 15.1 The Web Development Infrastructure 303
- 15.2 Creating Content for the WWW 305
- 15.3 Preparing Apache for Perl 310
- 15.4 Sending Data to a Web Server 315
- 15.5 Web Databases 320
- 16 Web Automation 329
- 16.1 Why Automate Surfing? 329
- 16.2 Automated Surfing with Perl 330
- IV Working with Applications 337
- 17 Tools and Datasets 339
- 17.2 Sequence Databases 340
- 17.3 General Concepts and Methods 347
- 17.4 Introducing Bioinformatics Tools 357
- 17.5 BLAST 362
- 18 Applications 373
- 18.2 Scientific Background to Mer Operon 374
- 18.3 Downloading the Raw DNA Sequence 377
- 18.4 Initial BLAST Sequence Similarity Search 378
- 18.5 GeneMark 380
- 18.6 Structural Prediction with SWISS-MODEL 388
- 18.7 DeepView as a Structural Alignment Tool 396
- 18.8 PROSITE and Sequence Motifs 401
- 18.9 Phylogenetics 407
- 19 Data Visualisation 413
- 19.1 Introducing Visualisation 413
- 19.2 Displaying Tabular Data Using HTML 415
- 19.3 Creating High-quality Graphics with GD 422
- 19.4 Plotting Graphs 431
- 20 Introducing Bioperl 441
- 20.2 Bioperl's Relationship to Project Ensembl 442
- 20.3 Installing Bioperl 442
- 20.4 Using Bioperl: Fetching Sequences 444
- 20.5 Remote BLAST Searches 448.
- Notes:
- Includes bibliographical references (pages [461]-466) and index.
- Local Notes:
- Acquired for the Penn Libraries with assistance from the Class of 1924 Book Fund.
- ISBN:
- 047085331X
- OCLC:
- 55587854
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