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A GENE ONTOLOGY BASED COMPUTATIONAL APPROACH FOR THE PREDICTION OF PROTEIN FUNCTIONS

Kharsikar, Saket
http://rave.ohiolink.edu/etdc/view?acc_num=akron1187026388

Abstract Details

2007, Master of Science in Engineering, University of Akron, Biomedical Engineering.
Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotation and prediction become an essential and challenging task of post-genomic research. In this research, we present an automated protein function prediction system based on a set of proteins of known biological functions. The functions of the proteins are characterized with Gene Ontology (GO) annotations. The prediction system uses a novel measure to calculate the pair-wise overall similarity between protein sequences. The protein function prediction is performed based on the GO annotations of similar sequences using a weighted k-nearest neighbor method. We show the prediction accuracies obtained using the model organism yeast (Sacchyromyces cerevisiae). The results indicate that the weighted k-nearest neighbor method significantly outperforms the regular k-nearest neighbor method for protein biological function prediction.
Dale Mugler (Advisor)
PROTEIN; GENE; KNN; Clustering; k-nearest neighbor method; PROTEIN FUNCTIONS; k-nearest

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Citations

  • Kharsikar, S. (2007). A GENE ONTOLOGY BASED COMPUTATIONAL APPROACH FOR THE PREDICTION OF PROTEIN FUNCTIONS [Master's thesis, University of Akron]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=akron1187026388

    APA Style (7th edition)

  • Kharsikar, Saket. A GENE ONTOLOGY BASED COMPUTATIONAL APPROACH FOR THE PREDICTION OF PROTEIN FUNCTIONS. 2007. University of Akron, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=akron1187026388.

    MLA Style (8th edition)

  • Kharsikar, Saket. "A GENE ONTOLOGY BASED COMPUTATIONAL APPROACH FOR THE PREDICTION OF PROTEIN FUNCTIONS." Master's thesis, University of Akron, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=akron1187026388

    Chicago Manual of Style (17th edition)

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© 2007, all rights reserved.
This open access ETD is published by University of Akron and OhioLINK.