Building Phylogenetic Trees Based on Biochemical Pathways

.................................................................................................................... 1 Abbreviations............................................................................................................ 2 Chapter 1: Introduction.............................................................................................. 3 1.1. Motivation .................................................................................................. 3 1.2. Background ................................................................................................ 4 1.2.1. Metabolic pathway alignment............................................................. 4 1.2.2. Building phylogenetic trees ................................................................ 4 1.2.3. Using a computational grid................................................................. 4 1.3. Metabolic pathway data sources.................................................................. 4 1.4. Previous work ............................................................................................. 6 1.5. Highlights of results.................................................................................... 7 1.6. Outline........................................................................................................ 8 Chapter 2: Method..................................................................................................... 9 2.1. Pathway alignment and arranging the data .................................................. 9 2.2. Using a computational grid ....................................................................... 10 2.3. Interpreting and weighting the data ........................................................... 11 2.4. Building phylogenetic trees....................................................................... 13 2.5. Computational pipeline Pseudo-code ........................................................ 13 Chapter 3: Results ................................................................................................... 15 3.1. The data sources ....................................................................................... 15 3.2. Full data results......................................................................................... 15 3.3. Benchmarks results ................................................................................... 16 3.3.1. Archaea benchmark (BM1) results ................................................... 18 3.3.2. Bacteria benchmark (BM2) results ................................................... 19 3.3.3. Mixed benchmark (BM3) results ...................................................... 20 Chapter 4: Discussion.............................................................................................. 21 Chapter 5: Future work............................................................................................ 23 Bibliography ........................................................................................................... 24 Appendix A............................................................................................................. 26 Appendix B............................................................................................................. 30 T ec hn io n C om pu te r Sc ie nc e D ep ar tm en t M .S c. T he si s M SC -2 00 823 2 00 8