Bioinformatics Biocomputing and Perl An Introduction to Bioinformatics Computing Skills and Practice
, by Moorhouse, Michael; Barry, PaulNote: Supplemental materials are not guaranteed with Rental or Used book purchases.
- ISBN: 9780470853313 | 047085331X
- Cover: Paperback
- Copyright: 7/2/2004
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.
<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’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).
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. |
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