Date of Award

4-2012

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Computer Science

First Advisor

Dhundy Bastola

Second Advisor

Sanjukta Bhowmick

Third Advisor

Zhengxin Chen

Abstract

Advances in sequencing technology have resulted in the sequencing of whole genomes from many simple organisms such as fungi and bacteria, while allowing the assembly of much more complex genomes like humans and chimpanzees. Consequently, association of segments of newly sequenced genomes to specific function (i.e. annotation) is being completed by comparative study of protein coding regions from previously annotated genome data. While this is an ideal procedure to process and annotate huge number of available genomic sequences, this approach can potentially lead to propagating erroneous annotation in a public sequence repository and vastly diminish the integrity of these new annotation of genome sequences. In this project, the Wrongly Annotated Protein identification System (WRAPS) has been created to analyze previously annotated proteins quickly and efficiently. The likeliness that the protein is correctly annotated is determined by weighted scoring schema based on conservation of protein domain, the domains present in different reading frames, and isoelectric point. A study of 88,023 proteins of Yersinia, Staphylococcus, and Bacillus using WRAPS show that there are several proteins that can be considered wrongly annotated, as well as the correctness of annotation among these proteins.

Comments

A Thesis Presented to the Department of Computer Science and the Faculty of the Graduate College University of Nebraska In Partial Fulfillment Of the Requirements for the Degree Master of Science University of Nebraska at Omaha. Copyright 2012 Benjamin K. Nelson.

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