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

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ISBN-10: 047085331X

ISBN-13: 9780470853313

Edition: 2004

Authors: Michael Moorhouse, Paul Barry

List price: $120.95
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Description:

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 bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl 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…    
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Book details

List price: $120.95
Copyright year: 2004
Publisher: John Wiley & Sons, Incorporated
Publication date: 7/2/2004
Binding: Paperback
Pages: 508
Size: 7.54" wide x 8.78" long x 1.23" tall
Weight: 1.936
Language: English

Preface
Setting the Biological Scene
Introducing Biological Sequence Analysis
Protein and Polypeptides
Generalised Models and their Use
The Central Dogma of Molecular Biology
Genome Sequencing
The Example DNA-gene-protein system we will use
Where to from Here
Setting the Technological Scene
The Layers of Technology
Finding per
Where to from Here
Working with Perl
The Basics
Let's Get Started!
Iteration
More Iterations
Selection
There Really is MTOWTDI
Processing Data Files
Introducing Patterns
Where to from Here
The Maxims Repeated
Places to Put Things
Beyond Scalars
Arrays: Associating Data with Numbers
Hashes: Associating Data with Words
Where to from Here
The Maxims Repeated
Getting Organised
Named Blocks
Introducing Subroutines
Creating Subroutines
Visibility and Scope
In-built Subroutines
Grouping and Reusing Subroutines
The Standard Modules
CPAN: The Module Repository
Where to from Here
The Maxims Repeated
About Files
I/O: Input and Output
Reading Files
Writing Files
Chopping and Chomping
Where to from Here
The Maxims Repeated
Patterns, Patterns and More Patterns
Pattern Basics
Introducing the Pattern Metacharacters
Anchors
The Binding Operators
Remembering What Was Matched
Greedy by Default
Alternative Pattern Delimiters
Another Useful Utility
Substitutions: Search and Replace
Finding a Sequence
Where to from Here
The Maxims Repeated
Perl Grabbag
Introduction
Strictness
Perl One-liners
Running Other Programs from per
Recovering from Errors
Sorting
HERE Documents
Where to from Here
The Maxims Repeated
Working with Data
Downloading Datasets
Let's Get Data
Downloading from the Web
Where to from Here
The Maxims Repeated
The Protein Databank
Introduction
Determining Biomolecule Structures
The Protein Databank
The PDB Data-file Formats
Accessing Data in PDB Entries
Accessing PDB Annotation Data
Contact Maps
STRIDE: Secondary Structure Assignment
Assigning Secondary Structures
Introducing the mmCIF Protein Format
Where to from Here
The Maxims Repeated
Non-redundant Datasets
Introducing Non-redundant Datasets
Non-redundant Protein Structures
Where to from Here
The Maxims Repeated
Databases
Introducing Databases
Available Database Systems
SQL: the Language of Databases
A Database Case Study: MER
Where to from Here
The Maxims Repeated
Databases and Perl
Why Program Databases?
Perl Database Technologies
Preparing Perl
Programming Databases with DBI
Customising Output
Customising Input
Extending SQL
Where to from Here
The Maxims Repeated
Working with the Web
The Sequence Retrieval System
An Example of What's Possible
Why SRS?
Using SRS
Where to from Here
The Maxims Repeated
Web Technologies
The Web Development Infrastructure
Creating Content for the WWW
Preparing Apache for Perl
Sending Data to a Web Server
Web Databases
Where to from Here
The Maxims Repeated
Web Automation
Why Automate Surfing?
Automated Surfing with Perl
Where to from Here
The Maxims Repeated
Working with Applications
Tools and Datasets
Introduction
Sequence Databases
General Concepts and Methods
Introducing Bioinformatics Tools
BLAST
Where to from Here
The Maxims Repeated
Applications
Introduction
Scientific Background to Mer Operon
Downloading the Raw DNA Sequence
Initial BLAST Sequence Similarity Search
GeneMark
Structural Prediction with SWISS-MODEL
DeepView as a Structural Alignment Tool
PROSITE and Sequence Motifs
Phylogenetics
Where to from Here?
The Maxims Repeated
Data Visualisation
Introducing Visualisation
Displaying Tabular Data Using HTML
Creating High-quality Graphics with GD
Plotting Graphs
Where to from Here
The Maxims Repeated
Introducing Bioperl
What is Bioperl?
Bioperl's Relationship to Project Ensembl
Installing Bioperl
Using Bioperl: Fetching Sequences
Remote BLAST Searches
Where to from Here
The Maxims Repeated
Appendix A
Appendix B
Appendix C
Appendix D
Appendix E
Appendix F
Index
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