An integrated comparative genomics environment

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What is Comparative Genomics?

Comparative genomics is a relatively new eld in biological research where genome sequences or genomic fragments are used (directly or indirectly) to compare various organisms.
This type of comparison allows scientists to study many aspects of an organisms biology including discovery of new genes and protein structure, evolution within and between species and many more (Cole, 1998; (1)). For example, understanding of our own genome has substantially increased after examining genetic feature counterparts in other organisms such as the mouse (Ureta-Vidal et al., 2003). When performing comparative genomics studies, researchers compare many dierent features contained within genomes such as genes, introns, conserved regions, repeat regions, re-arrangements and single nucleotide polymorphisms (SNPs) to make inferences about the evolution,
physiology, pathogenicity (Mulder et al., 2008) and genetic structure (Badger & Olsen, 1999) of the organisms being studied.
The fact that the genomes of all organisms are comprised of the same building blocks i.e. DNA, means that one could essentially compare the genomes of highly similar organisms (for population genomics) as well as phenotypically diverse organisms for example, mouse and human, anenomes and whales, grasses and trees etc. Comparative genomics is indeed a useful and insightful area of study producing many new biological insights and scientic breakthroughs.
An overview of modern comparative genomics techniques will be presented in this chapter and further on in chapters 3 and 4, several innovative approaches developed in this project will also be presented.

1 Introduction
1.1 What is Comparative Genomics?
1.2 Sequencing technologies and the need for comparative genomics
1.3 Common Methods used in Comparative Genomics
1.3.1 Sequence Alignment & BLAST
1.3.2 Genome Alignment
1.3.3 Synteny
1.3.4 Gene-by-gene comparative genomics
1.3.5 Single Nucleotide Polymorphism analyses in comparative genomics
1.3.6 Phylogenetic Analyses
1.3.7 Regulatory Motif Discovery .
1.4 A Novel Comparative Genomic Technique using Oligonucleotide usage pattern proling
1.4.1 Codon Usage Bias .
1.4.2 Oligonucleotide Usage Bias
1.5 Conclusions
1.6 Problem Statement
1.7 Aims
2 An integrated comparative genomics environment
2.1 Introductio
2.2 FunGIMS
2.2.1 Overview of FunGIMS
2.2.2 Model
2.2.3 View
2.2.4 Controller
2.3 Examples of comparative genomics environments and what they have to oer
2.4 Requirements
2.4.1 User interface requireme
2.4.2 Analysis Requirements
2.4.3 Data structure requirements
2.5 Design Principles
2.6 Model-View-Controller Architecture and integration
2.7 Technical implementation details
2.8 Implementation of a general comparative genomics environment
3 The Seqword Genome Browser
3.1 Introduction
3.2 Background
3.3 Results
3.4 Identication of divergent genomic islands
3.5 Scientic Investigation Application to mycobacteria
3.6 Discussion
4 The Mycobacterial Comparison Project
4.1 Introduction
4.2 Tuberculosis
4.3 The Mycobacterial genome
4.4 Comparative genomics of Mycobacteria
4.5 The Mycobacterial Comparison Project in context
4.6 Data pre-processing
4.7 Database requirements
4.8 Graphical User Interface requirements
4.9 Workow summary
4.10 A comparative genomics investigation of key genomic loci in mycobacterial genomes
and their role in virulence
4.11 Discussion
5 Concluding Discussion