Bioinformatics algorithms and applications

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Bioinformatics has become an essential part of genomics and proteomics research.  Almost every type of biological and biochemical data needs to be analyzed using computers and special software tools.  The success of the wet lab experiments depend greatly on the sensitivity and accuracy of the algorithms and software employed for data analysis.  The proposed research program concerns the algorithm design and software development in bioinformatics. Because of the complexity of the data and unavoidable experimental errors, bioinformatics algorithm design and software development are challenging, yet very necessary.  The proposed research program will allow the applicant to continue his successful work into bioinformatics algorithm and software development.  The research will be focused on, but not limited to, the analyses of genomic sequence data and mass spectrometry data. Specifically, the research project will develop full-sensitive and high-speed homology search algorithm and software tools.  Currently the full-sensitive homology searches are performed with costly parallel computers.  The research potentially replaces the costly hardware solution with highly efficient software and inexpensive PCs.  The project will also develop software tools for identifying proteins and their modifications using tandem mass spectrometry data.  Protein identification is a fundamental step for almost all proteomics research and tandem mass spectrometry is a standard experimental method.  However, the existing software is insufficient.  This research has impact for drug development and other human-health related research.