.............................................................................................................................. III DECLARATION ........................................................................................................................IV ACKNOWLEDGEMENTS........................................................................................................ V LIST OF FIGURES....................................................................................................................VI LIST OF TABLES.................................................................................................................. VIII TABLE OF CONTENTS............................................................................................................. 1 CHAPTER 1 : MICROBIAL GENOMES, POSITIVE SELECTION AND BACTERIAL VIRULENCE ................................................................................................................................ 6 INTRODUCTION............................................................................................................................ 6 MICROBIAL GENOMES – KNOWLEDGE, APPLICATIONS, LIMITATIONS ......................................... 7 FORCES SHAPING MICROBIAL GENOME EVOLUTION ................................................................... 9 POSITIVE SELECTION: THEORY AND IMPLEMENTATION............................................................. 11 BACTERIAL PATHOGENS AND VIRULENCE................................................................................. 13 DETERMINATION OF BACTERIAL GENES SUBJECT TO DIVERSIFYING SELECTION...................... 15 CHAPTER 2 : METHODS AND MATERIALS..................................................................... 19 INTRODUCTION.......................................................................................................................... 19 BACTERIAL SEQUENCES............................................................................................................ 20 PRE-PROCESSING OF GENBANK BACTERIAL SEQUENCE FILES.................................................. 20 POSITIVE SELECTION DETECTION PIPELINE............................................................................... 22 Orthologue Identification ..................................................................................................... 22 Generation of In – Frame Codon Aligned Sequences .......................................................... 24 Assay for Positive Selection................................................................................................. 24 Annotation of Bacterial Genes under Positive Selection ..................................................... 25 CURATION OF ALIGNMENTS FOR GENES UNDER POSITIVE SELECTION ...................................... 25 VIRULENCE GENE DATA MINING .............................................................................................. 27 BACTERIAL GENE LISTS............................................................................................................ 28 BACTERIAL GENE FEATURES..................................................................................................... 28 GENE ONTOLOGY ANNOTATION OF BACTERIAL GENE LISTS.................................................... 29