Date of Award

2015

Degree Type

Thesis

Degree Name

Master of Science in Computer Science

Department

Computer Science and Statistics

First Advisor

Joan Peckham

Abstract

The idea behind the AMPed database is to create an annotated collection of information about antimicrobial peptides derived from several existing larger and heterogeneous databases with the goal of uniformity and coherence. It will be an open source bioinformatics tool that researchers will be able to use in order to find and download genomic sequences relevant to their research, as well as obtaining links to the original data source. This thesis will discuss the original AMPed concept, the database’s conceptual (ER – Entity-Relationship) design, the design and implementation of the database tables, and the Bioparser software tool for importing the data into the database. Before this work Dr. Martin of the University of Rhode Island and her students began this project by creating a preliminary design of the database. In addition a tool to extract relevant data from PDB (Protein Data Bank) XML files was developed. This work was informative, but none of the previous solutions were ultimately used in this project. Along with the design of the AMPed database, a bioparser software tool to parse and import bulk data was built by our team. In the future, prediction tools that are tailored to the needs of the peptide research community will need to be developed, but this is outside of the scope of this thesis. Furthermore, the AMPed group is developing a secure web interface alongside the completion of the thesis. This web interface work is supervised by Dr. Martin and advised by George Konstantinidis.

Share

COinS