Development and Testing of Algorithmic Solutions for Problems in Computational Genomics and Proteomics

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Development and Testing of Algorithmic Solutions for Problems in Computational Genomics and Proteomics

Thiruvarangan Ramaraj-2010-01-01-Montana State University ScholarWorks (Montana State University)

TL;DRAbstract

This dissertation covers three subjects: (i) computational characterization of Antigen (Ag)-Antibody (Ab) interactions (ii) a novel and effective algorithm to predict the epitope of a protein based on an antibody imprinting technique (iii) a comparison of existing de novo genome assembler algorithms targeted specifically at the assembly of data generated by Illumina (Solexa) short-read sequencing technology, and suggestions for their improvement. The first part focuses on identification, characterization and understanding the ways in which the antibodies and antigens interact. We analyze Epitope/Paratope region using a large dataset of Ag - Ab complex structural data taken from the PDB. Epitope/Paratope regions in our dataset have been characterized in terms of their size, average amino acid residue composition, residue-residue pairing preferences, and residue dispersion in the epitope and paratope regions. This analysis provides a more up-to-date picture of the Ag-Ab interface and pro

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This dissertation covers three subjects: (i) computational characterization of Antigen (Ag)-Antibody (Ab) interactions (ii) a novel and effective algorithm to predict the epitope of a protein based on an antibody imprinting technique (iii) a comparison of existing de novo genome assembler algorithms targeted specifically at the assembly of data generated by Illumina (Solexa) short-read sequencing technology, and suggestions for their improvement. The first part focuses on identification, characterization and understanding the ways in which the antibodies and antigens interact. We analyze Epitope/Paratope region using a large dataset of Ag - Ab complex structural data taken from the PDB. Epitope/Paratope regions in our dataset have been characterized in terms of their size, average amino acid residue composition, residue-residue pairing preferences, and residue dispersion in the epitope and paratope regions. This analysis provides a more up-to-date picture of the Ag-Ab interface and pro

Keywords

Computer scienceComputational genomicsGenomicsData scienceBiological networkBiological dataSystems biologyTheoretical computer science

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