Sequence Alignment Based Techniques for RNA Viruses Research

In recent years, many emerging viruses are found in the world and they cause calamities at various countries and seasons. Most of these emerging viruses, such as SARS, belong to the RNA virus. In general, the mutation rate of a RNA virus is faster than that of a DNA virus and it is very important to develop related techniques for RNA viruses in order to avoid next possible super-virus which may be happened in the future. The goal of the integrated project is to discovery sequence, structure, function and evolution for RNA Viruses, especially for Influenza and Enterovirus. The goal of this sub-project is tried to do the research for RNA viruses by sequence alignment based techniques and focuses on discovering sequence and evolution relationships for RNA viruses. We will develop new multiple sequence alignment techniques; do the compare genomic research for RNA viruses or their hosts; and scanning large scale sequences or whole genomes of RNA viruses. The descriptions of goals for each year in this sub-project are listed below. First year, we will develop new multiple sequence alignment techniques by integrating global three-sequence alignment technique, local three-sequence alignment technique and three-profile alignment technique. These techniques will be extended to be useful for DNA, RNA and Protein sequences. The useful website server with these techniques also will be built for biologists. Second year, we will do the compare genomic research for RNA viruses which is focused on sequence conserved, sequence variation and evolution relationship. We also will do the compare genomic research for RNA viruses’ hosts to analyze the conserved and the variation for the receptors. In this year, the useful website server to do the comparisons also will be built for biologists. Third year, we will try to scan large scale sequences or whole genomes of RNA viruses. By this requirement, we will develop parallel techniques and divide and conquer schemes for proposed techniques in the last two years. We also will propose some possible hypotheses for RNA viruses and then try to prove them by some tests. In the end of third year, a database with the results of compare genomic research will be built for biologists.

Project ID:PB9801-2180
External Project ID:NSC97-2221-E182-033-MY3