The Design, Construction And Implementation Of Genomic Analysis Platform For Mycobacterium

The unique bacterial genus Mycobacterium has a tremendous impact on human society, for example there are millions of human infections and even death caused by its model species Mycobacterium tuberculosis. The mycobacterial pathogenesis studies are cucial for the development of drugs and vaccines against it. With the wide applications of high throughput sequencing technology, microbiological research has changed its methodology from phenotype-to-gene to sequence-to-function. The publication of the first complete genome of mycobacterial strain Mycobacterium tuberculosis H37Rv in 1998 opens the genomic era of mycobacterial research. Genomic data greatly accelerate the gene function studies of Mycobacterium. For example, the studies of mycobacterial genome polymorphism using whole genome tilling array become a hot area in mycobacterial research. In addition, the invention of new genetic approaches makes the identification of new mycobacterial genes which play pivotal roles in the infection and pathogenesis much more easier. The accumulation of large amount of genomic data in mycobacterial research makes the management and utilization a challenge.The work in this thesis is about the collection, curation and integration of large amount of mycobacterial genomic data based on manual literature investigation and careful requirement analysis. Besides, with the development of embedded user-friendly and powerful tools, we provide the the mycobacterial research community a comprehensive and highly integrated genomic analysis platform. The platform includes not only regular genomic information, such as genome sequences and annotations, but also experimental genome polymorphism data both from public resources and our own lab. More importantly, we collected and curated various sorts of functional genomic data, like virulence genes, essential gnes and operon structure etc. The powerful toolkit in the platform enables users not only to quick find the data they want but also do some anlysis job, such as genome visualization and comparison. Users can also upload their own data into the platform, and thus make the data content most up-to-date.The completion and publication of our platform will be helpful for researchers to better understand the unique virulence mechanism, pathogenesis, genome structures and molecular evolution of Mycobacterium.