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Computer Science and Engineering: Theses, Dissertations, and Student Research

Biochemistry, Biophysics, and Structural Biology

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Full-Text Articles in Computer Engineering

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene Jul 2016

Use Of Clustering Techniques For Protein Domain Analysis, Eric Rodene

Computer Science and Engineering: Theses, Dissertations, and Student Research

Next-generation sequencing has allowed many new protein sequences to be identified. However, this expansion of sequence data limits the ability to determine the structure and function of most of these newly-identified proteins. Inferring the function and relationships between proteins is possible with traditional alignment-based phylogeny. However, this requires at least one shared subsequence. Without such a subsequence, no meaningful alignments between the protein sequences are possible. The entire protein set (or proteome) of an organism contains many unrelated proteins. At this level, the necessary similarity does not occur. Therefore, an alternative method of understanding relationships within diverse sets of proteins ...


Clustering And Classification Of Multi-Domain Proteins, Neethu Shah Dec 2013

Clustering And Classification Of Multi-Domain Proteins, Neethu Shah

Computer Science and Engineering: Theses, Dissertations, and Student Research

Rapid development of next-generation sequencing technology has led to an unprecedented growth in protein sequence data repositories over the last decade. Majority of these proteins lack structural and functional characterization. This necessitates design and development of fast, efficient, and sensitive computational tools and algorithms that can classify these proteins into functionally coherent groups.

Domains are fundamental units of protein structure and function. Multi-domain proteins are extremely complex as opposed to proteins that have single or no domains. They exhibit network-like complex evolutionary events such as domain shuffling, domain loss, and domain gain. These events therefore, cannot be represented in the ...