Bioinformatics : principles and applications

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Contents
Part One Principles
	1. Web-based Sequence Analysis: BLAST I
		1.1 Basic Local Alignment Search Tool (BLAST)
		1.2 The Purpose of BLAST
		1.3 Terminology
		1.4 BLAST Analysis
		1.5 BLAST 2
		1.6 Automated Alignments with Perl
			References
	2. Web-based Sequence Analysis: BLAST II
		2.1 Basic Local Alignment Search Tool (BLAST)
		2.2 Scoring Matrices
		2.3 PAM or Per cent Accepted Mutation Matrices
		2.4 BLOSUM (Blocks Substitution Matrices)
		2.5 The Relationship between BLOSUM and PAM Substitution Matrices
		2.6 Working of the BLAST Algorithm
		2.7 A Practical BLASTN Exercise
		2.8 Explanation of the BLAST Output
		2.9 Advanced BLASTN
		2.10 Biological Analysis of BLASTN: Cystic Fibrosis
		2.11 Automating BLAST Analyses with Perl
	3. Web-based Sequence Analysis: BLAST III
		3.1 Standalone BLAST
		3.2 Configuring blastall
		3.3 Downloading Databases from NCB!
		3.4 Formatting NCBI's Databases
		3.5 Running blastall
		3.6 Downloading Pre-formatted Databases
		3.7 fastacmd
		3.8 bl2seq
		3.9 Performing Local BLAST Searches with Perl
		3.10 Sequence Annotation
	4. Web-based Sequence Analysis: Gene Prediction
		4.1 Introduction
		4.2 Terminology and Concepts
		4.3 Gene Prediction Programs
		4.4 GenScan
		4.5 Running GenScan Analyses
		4.6 Analyzing GenScan Output
		4.7 GenScan Analysis with LWP::UserAgent
	5. Web-based Sequence Analysis: HMMER .
		5.1 Introduction
		5.2 Downloading HMMER
		5.3 Why use HMMER?
		5.4 Running HMMER Commands
		5.5 HMMER: A Practical Example
		5.6 HMMER Utilities
			References
	6. PSI-BLAST
		6.1 Introduction
		6.2 PSI-BLAST and Protein Analysis
		6.3 When is PSI-BLAST better than BLASTP?
		6.4 The Design of PSI-BLAST
		6.5 Advantages of PSI-BLAST
		6.6 Limitations of PSI-BLAST
		6.7 Example of a PSI-BLAST Search
Part Two Applications
	7. Accessing Sequence Information Using BioPerl
		7.1 BioPer! Installation
		7.2 BioPer! Modules
		7.3 Object Oriented Programming
		7.4 Using BioPer!
		7.5 The write_seqO Function
		Appendix I: Installing External Modules
		Appendix II: Upgrading BioPer!
		Appendix III: Testing for Availability of Individual Modules
	8. Bio::DB::GenBank
		8.1 Introduction
		8.2 Structure of a GenBank Record
		8.3 The Bio::DB::GenBank Module
	9. Accessing GenBank Data
		9.1 Introduction
		9.2 GenBank Tags
		9.3 Extracting Tags and their Values
		9.4 Sample Scripts
	10. BioPerl BLAST Modules.
		10.1 Introduction
		10.2 BLAST Programs
		10.3 BLAST 2
		10.4 Per! Modules for BLAST2
		10.5 Using BioPer! for BLAST2
		10.6 Standalone BLAST
		10.7 Configuring blastall
		10.8 Bio::Tools::Run::StandAloneBlast
		10.9 Performing BLAST Searches
		10.10 Formatting NCBI's Databases
		10.11 Running blastall
		10.12 Running BLAST with Bio::Tools::Run::StandAloneBlast
	11. Parsing BLAST Output
		11.1 Generating a Raw BLAST Report
		11.2 The Bio::Tools::Blast Module
		11.3 Parsing the HPR BLAST Report
		11.4 Specifying a Filter Function
		11.5 Formatting Parsing Results into a Table or HTML
Index