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Bioinformatics Biocomputing and Perl : An Introduction to Bioinformatics Computing Skills and Practice - Michael Moorhouse

Bioinformatics Biocomputing and Perl

An Introduction to Bioinformatics Computing Skills and Practice

Paperback Published: 1st July 2004
ISBN: 9780470853313
Number Of Pages: 508

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<i>Bioinformatics, Biocomputing and Perl</i> 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&#8217;s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. <p> <b>Working with Perl</b> presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. <p> <b>Working with Data</b> applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. <p> <b>Working with the Web</b> presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. <p> <b>Working with Applications</b> shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

"...such a helpful and relevant book...I would have been at a complete loss without your book!" (Susan Tzotzos MSc, PhD, Vienna, Austria)

Prefacep. xv
Setting the Biological Scenep. 1
Introducing Biological Sequence Analysisp. 1
Protein and Polypeptidesp. 4
Generalised Models and their Usep. 5
The Central Dogma of Molecular Biologyp. 6
Genome Sequencingp. 10
The Example DNA-gene-protein system we will usep. 12
Where to from Herep. 13
Setting the Technological Scenep. 15
The Layers of Technologyp. 15
Finding perp. 17
Where to from Herep. 18
Working with Perlp. 19
The Basicsp. 21
Let's Get Started!p. 21
Iterationp. 26
More Iterationsp. 30
Selectionp. 34
There Really is MTOWTDIp. 36
Processing Data Filesp. 41
Introducing Patternsp. 44
Where to from Herep. 46
The Maxims Repeatedp. 46
Places to Put Thingsp. 49
Beyond Scalarsp. 49
Arrays: Associating Data with Numbersp. 49
Hashes: Associating Data with Wordsp. 60
Where to from Herep. 68
The Maxims Repeatedp. 68
Getting Organisedp. 71
Named Blocksp. 71
Introducing Subroutinesp. 73
Creating Subroutinesp. 74
Visibility and Scopep. 85
In-built Subroutinesp. 90
Grouping and Reusing Subroutinesp. 92
The Standard Modulesp. 96
CPAN: The Module Repositoryp. 96
Where to from Herep. 100
The Maxims Repeatedp. 100
About Filesp. 103
I/O: Input and Outputp. 103
Reading Filesp. 105
Writing Filesp. 116
Chopping and Chompingp. 118
Where to from Herep. 119
The Maxims Repeatedp. 119
Patterns, Patterns and More Patternsp. 121
Pattern Basicsp. 121
Introducing the Pattern Metacharactersp. 124
Anchorsp. 132
The Binding Operatorsp. 134
Remembering What Was Matchedp. 135
Greedy by Defaultp. 137
Alternative Pattern Delimitersp. 138
Another Useful Utilityp. 139
Substitutions: Search and Replacep. 140
Finding a Sequencep. 142
Where to from Herep. 146
The Maxims Repeatedp. 146
Perl Grabbagp. 147
Introductionp. 147
Strictnessp. 147
Perl One-linersp. 149
Running Other Programs from perp. 152
Recovering from Errorsp. 153
Sortingp. 155
HERE Documentsp. 159
Where to from Herep. 160
The Maxims Repeatedp. 161
Working with Datap. 163
Downloading Datasetsp. 165
Let's Get Datap. 165
Downloading from the Webp. 165
Where to from Herep. 171
The Maxims Repeatedp. 171
The Protein Databankp. 173
Introductionp. 173
Determining Biomolecule Structuresp. 174
The Protein Databankp. 177
The PDB Data-file Formatsp. 179
Accessing Data in PDB Entriesp. 182
Accessing PDB Annotation Datap. 183
Contact Mapsp. 192
STRIDE: Secondary Structure Assignmentp. 196
Assigning Secondary Structuresp. 197
Introducing the mmCIF Protein Formatp. 205
Where to from Herep. 210
The Maxims Repeatedp. 210
Non-redundant Datasetsp. 211
Introducing Non-redundant Datasetsp. 211
Non-redundant Protein Structuresp. 213
Where to from Herep. 217
The Maxims Repeatedp. 217
Databasesp. 219
Introducing Databasesp. 219
Available Database Systemsp. 224
SQL: the Language of Databasesp. 226
A Database Case Study: MERp. 227
Where to from Herep. 269
The Maxims Repeatedp. 269
Databases and Perlp. 273
Why Program Databases?p. 273
Perl Database Technologiesp. 274
Preparing Perlp. 275
Programming Databases with DBIp. 276
Customising Outputp. 282
Customising Inputp. 285
Extending SQLp. 289
Where to from Herep. 292
The Maxims Repeatedp. 292
Working with the Webp. 295
The Sequence Retrieval Systemp. 297
An Example of What's Possiblep. 297
Why SRS?p. 298
Using SRSp. 298
Where to from Herep. 300
The Maxims Repeatedp. 300
Web Technologiesp. 303
The Web Development Infrastructurep. 303
Creating Content for the WWWp. 305
Preparing Apache for Perlp. 310
Sending Data to a Web Serverp. 315
Web Databasesp. 320
Where to from Herep. 327
The Maxims Repeatedp. 327
Web Automationp. 329
Why Automate Surfing?p. 329
Automated Surfing with Perlp. 330
Where to from Herep. 335
The Maxims Repeatedp. 336
Working with Applicationsp. 337
Tools and Datasetsp. 339
Introductionp. 339
Sequence Databasesp. 340
General Concepts and Methodsp. 347
Introducing Bioinformatics Toolsp. 357
BLASTp. 362
Where to from Herep. 371
The Maxims Repeatedp. 371
Applicationsp. 373
Introductionp. 373
Scientific Background to Mer Operonp. 374
Downloading the Raw DNA Sequencep. 377
Initial BLAST Sequence Similarity Searchp. 378
GeneMarkp. 380
Structural Prediction with SWISS-MODELp. 388
DeepView as a Structural Alignment Toolp. 396
PROSITE and Sequence Motifsp. 401
Phylogeneticsp. 407
Where to from Here?p. 410
The Maxims Repeatedp. 411
Data Visualisationp. 413
Introducing Visualisationp. 413
Displaying Tabular Data Using HTMLp. 415
Creating High-quality Graphics with GDp. 422
Plotting Graphsp. 431
Where to from Herep. 439
The Maxims Repeatedp. 439
Introducing Bioperlp. 441
What is Bioperl?p. 441
Bioperl's Relationship to Project Ensemblp. 442
Installing Bioperlp. 442
Using Bioperl: Fetching Sequencesp. 444
Remote BLAST Searchesp. 448
Where to from Herep. 451
The Maxims Repeatedp. 452
Appendix Ap. 453
Appendix Bp. 457
Appendix Cp. 459
Appendix Dp. 461
Appendix Ep. 467
Appendix Fp. 471
Indexp. 475
Table of Contents provided by Rittenhouse. All Rights Reserved.

ISBN: 9780470853313
ISBN-10: 047085331X
Audience: Tertiary; University or College
Format: Paperback
Language: English
Number Of Pages: 508
Published: 1st July 2004
Publisher: John Wiley and Sons Ltd
Country of Publication: US
Dimensions (cm): 23.4 x 19.1  x 2.5
Weight (kg): 0.93