Document Type


Publication Date

Spring 5-1-2007


Computer Science

First Advisor

Rob Knight


Alignment and detection of syntenic regions of genes can lead to a better understanding of evolution, both at the species level and at the level of individual genes. In particular, understanding the evolution of genomic features can lead to a better understanding of the genetic changes involved in pathogenicity. Knowing when genes were gained or lost, and whether they were gained or lost together, is important for understanding and predicting their association in functional pathways. In this thesis, I compared the compositional statistics of horizontally transferred islands to the species through codon usage biases and GC content. I also investigated the accuracy of algorithms to align circularly and randomly permuted simulated genomic islands. Detection of horizontally transferred genes will aid in phylogenetic research because these genes violate the mathematical models of sequence evolution typically used for phylogenetic reconstruction. Furthermore, since many of the genes horizontally transferred are involved in antibiotic resistance and pathogenesis, better methods of detection will also aid in medical research.