Comparative genomics exploration tools

Comparative Genomics focuses on elucidating the genetic differences between different species or different strains of the same species by the comparative analysis of DNA sequences to identify functional elements and regulatory regions. This thesis describes the design and development of two software tools to support comparative genomics research. These tools were specifically developed to support the analysis and assembly of sequence data produced from innovative new DNA sequencing technology from 454 Life Sciences using the PicoTiterPlate(TM) device. This technology will dramatically affect comparative genomics research. Currently available software tools were developed to handle traditional shotgun sequences averaging 500-1000 base pairs in length. These tools are inadequate to handle the unique characteristics of sequence reads generated by 454 Life Sciences. The goal of this research is to adapt currently available tools and develop new tools to be used for sequence reads generated by any sequencing technology, even those having different characteristics from the traditional shotgun sequences