CAREER: Computational Protein Function Annotation for Metagenomics

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"This award is funded under the American Recovery and Reinvestment Act of 2009(Public Law 111-5)."This is a CAREER award to Dr. Yuzhen Ye of the Department of Informatics at Indiana University. Dr Ye is a second-year tenure track Assistant Professor. Metagenomic sequences are vast in number and as obtained in the lab, fragmented and short (due to the limitations of sequencing techniques). The complexity of metagenomics data can also be overwhelming, as it contains sequences (by random sampling) from different individuals of different species, or different strains of the same species living in the same niche. As a result, many of the computational methods that have contributed to the success of numerous individual organismal genome projects are not directly applicable to metagenomics projects. New computational methods need to be developed to optimize the analysis of metagenomic sequence data and advance the field. This grant to Dr. Ye will develop computational protein function annotation of metagenomic sequence data to improve functional annotation of metagenomic sequence data. In this project, software is being designed and developed for improved protein sequence prediction by using ORF (Open Reading Frame) assembly and by specifically designing a gene finder for DNA fragments that can tolerate sequencing errors. Annotations of various biological functions including biological pathways, transmembrane transporters and enzymes are being carried out with computational tools. Exploratory projects are being developed to test several ideas for utilizing metagenomic sequence data to improve function annotation methods. Several computational tools and pipelines, designed specifically for metagenomic sequence data analysis, will be released as open access (e.g., through collaboration with CAMERA). The tools will be available through the Ye lab website:http://mendel.informatics.indiana.edu/~yye/lab/index.phpAs a part of her CAREER award, Dr. Ye will develop highly-integrated activities using metagenomic science as a model for education-research integration. The PI is actively working with the Office of Strategic Mentoring (OSM), Alliances for Graduate Education and Professoriate Program (AGEP), Women in Science Program (WISP), and Women in Computing (WIC) organizations at Indiana University to recruit students into her program.