Bioinformatics Biocomputing and Perl An Introduction to Bioinformatics Computing Skills and Practice

by Moorhouse, Michael; Barry, Paul

• ISBN13: 9780470853313
• ISBN10: 047085331X
• Edition: 1st
• Format: Paperback
• Copyright: 2004-07-02
• Publisher: WILEY

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. Book jacket.

Author Biography

<b>Michael Moorhouse</b> works as a Bioinformatics Researcher for Erasmus MC in Rotterdam, The Netherlands. He holds a B.Sc. from UMIST and an M.Sc. from The University of Manchester. Michael recently completed a Ph.D. from The University of Birmingham in the UK. He has been involved in numerous bioinformatics courses throughout the UK and Netherlands. This is Michael&#8217;s first book. <p> <b>Paul Barry</b> works as a Lecturer in Computing Science at The Institute of Technology, Carlow in Ireland. He holds a B.Sc. from The University of Ulster in Jordanstown, Northern Ireland and recently completed an M.Sc. from The Institute of Technology, Sligo in Ireland. He is the author of <i>Programming the Network with Perl</i> (Wiley, 2002).

Table of Contents

Preface	p. xv
Setting the Biological Scene	p. 1
Introducing Biological Sequence Analysis	p. 1
Protein and Polypeptides	p. 4
Generalised Models and their Use	p. 5
The Central Dogma of Molecular Biology	p. 6
Genome Sequencing	p. 10
The Example DNA-gene-protein system we will use	p. 12
Where to from Here	p. 13
Setting the Technological Scene	p. 15
The Layers of Technology	p. 15
Finding per	p. 17
Where to from Here	p. 18
Working with Perl	p. 19
The Basics	p. 21
Let's Get Started!	p. 21
Iteration	p. 26
More Iterations	p. 30
Selection	p. 34
There Really is MTOWTDI	p. 36
Processing Data Files	p. 41
Introducing Patterns	p. 44
Where to from Here	p. 46
The Maxims Repeated	p. 46
Places to Put Things	p. 49
Beyond Scalars	p. 49
Arrays: Associating Data with Numbers	p. 49
Hashes: Associating Data with Words	p. 60
Where to from Here	p. 68
The Maxims Repeated	p. 68
Getting Organised	p. 71
Named Blocks	p. 71
Introducing Subroutines	p. 73
Creating Subroutines	p. 74
Visibility and Scope	p. 85
In-built Subroutines	p. 90
Grouping and Reusing Subroutines	p. 92
The Standard Modules	p. 96
CPAN: The Module Repository	p. 96
Where to from Here	p. 100
The Maxims Repeated	p. 100
About Files	p. 103
I/O: Input and Output	p. 103
Reading Files	p. 105
Writing Files	p. 116
Chopping and Chomping	p. 118
Where to from Here	p. 119
The Maxims Repeated	p. 119
Patterns, Patterns and More Patterns	p. 121
Pattern Basics	p. 121
Introducing the Pattern Metacharacters	p. 124
Anchors	p. 132
The Binding Operators	p. 134
Remembering What Was Matched	p. 135
Greedy by Default	p. 137
Alternative Pattern Delimiters	p. 138
Another Useful Utility	p. 139
Substitutions: Search and Replace	p. 140
Finding a Sequence	p. 142
Where to from Here	p. 146
The Maxims Repeated	p. 146
Perl Grabbag	p. 147
Introduction	p. 147
Strictness	p. 147
Perl One-liners	p. 149
Running Other Programs from per	p. 152
Recovering from Errors	p. 153
Sorting	p. 155
HERE Documents	p. 159
Where to from Here	p. 160
The Maxims Repeated	p. 161
Working with Data	p. 163
Downloading Datasets	p. 165
Let's Get Data	p. 165
Downloading from the Web	p. 165
Where to from Here	p. 171
The Maxims Repeated	p. 171
The Protein Databank	p. 173
Introduction	p. 173
Determining Biomolecule Structures	p. 174
The Protein Databank	p. 177
The PDB Data-file Formats	p. 179
Accessing Data in PDB Entries	p. 182
Accessing PDB Annotation Data	p. 183
Contact Maps	p. 192
STRIDE: Secondary Structure Assignment	p. 196
Assigning Secondary Structures	p. 197
Introducing the mmCIF Protein Format	p. 205
Where to from Here	p. 210
The Maxims Repeated	p. 210
Non-redundant Datasets	p. 211
Introducing Non-redundant Datasets	p. 211
Non-redundant Protein Structures	p. 213
Where to from Here	p. 217
The Maxims Repeated	p. 217
Databases	p. 219
Introducing Databases	p. 219
Available Database Systems	p. 224
SQL: the Language of Databases	p. 226
A Database Case Study: MER	p. 227
Where to from Here	p. 269
The Maxims Repeated	p. 269
Databases and Perl	p. 273
Why Program Databases?	p. 273
Perl Database Technologies	p. 274
Preparing Perl	p. 275
Programming Databases with DBI	p. 276
Customising Output	p. 282
Customising Input	p. 285
Extending SQL	p. 289
Where to from Here	p. 292
The Maxims Repeated	p. 292
Working with the Web	p. 295
The Sequence Retrieval System	p. 297
An Example of What's Possible	p. 297
Why SRS?	p. 298
Using SRS	p. 298
Where to from Here	p. 300
The Maxims Repeated	p. 300
Web Technologies	p. 303
The Web Development Infrastructure	p. 303
Creating Content for the WWW	p. 305
Preparing Apache for Perl	p. 310
Sending Data to a Web Server	p. 315
Web Databases	p. 320
Where to from Here	p. 327
The Maxims Repeated	p. 327
Web Automation	p. 329
Why Automate Surfing?	p. 329
Automated Surfing with Perl	p. 330
Where to from Here	p. 335
The Maxims Repeated	p. 336
Working with Applications	p. 337
Tools and Datasets	p. 339
Introduction	p. 339
Sequence Databases	p. 340
General Concepts and Methods	p. 347
Introducing Bioinformatics Tools	p. 357
BLAST	p. 362
Where to from Here	p. 371
The Maxims Repeated	p. 371
Applications	p. 373
Introduction	p. 373
Scientific Background to Mer Operon	p. 374
Downloading the Raw DNA Sequence	p. 377
Initial BLAST Sequence Similarity Search	p. 378
GeneMark	p. 380
Structural Prediction with SWISS-MODEL	p. 388
DeepView as a Structural Alignment Tool	p. 396
PROSITE and Sequence Motifs	p. 401
Phylogenetics	p. 407
Where to from Here?	p. 410
The Maxims Repeated	p. 411
Data Visualisation	p. 413
Introducing Visualisation	p. 413
Displaying Tabular Data Using HTML	p. 415
Creating High-quality Graphics with GD	p. 422
Plotting Graphs	p. 431
Where to from Here	p. 439
The Maxims Repeated	p. 439
Introducing Bioperl	p. 441
What is Bioperl?	p. 441
Bioperl's Relationship to Project Ensembl	p. 442
Installing Bioperl	p. 442
Using Bioperl: Fetching Sequences	p. 444
Remote BLAST Searches	p. 448
Where to from Here	p. 451
The Maxims Repeated	p. 452
Appendix A	p. 453
Appendix B	p. 457
Appendix C	p. 459
Appendix D	p. 461
Appendix E	p. 467
Appendix F	p. 471
Index	p. 475
Table of Contents provided by Rittenhouse. All Rights Reserved.