Date of Award

12-2005

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Computer Engineering and Sciences

First Advisor

Debasis Mitra

Abstract

Sequence comparison is one of the most primitive operations used in bio-informatics. It is used as a basis for many other complex manipulations in the field of Computational Molecular Biology. Many methods and algorithms were developed to compare and align sequences effectively. Most of these methods use linear comparison and some standard scoring schemes to calculate the similarity between sequences. We described an alternative approach to compare sequences based on the correlogram method. This method has already been used in the past for comparing images. By using the correlogram method, a sequence is projected on a 3-D space and the difference between two sequences is calculated. This research describes construction of a correlogram and how correlograms can be used for sequence comparison. It also adds additional functionality to the basic correlogram method. Experiments with protein sequences corresponding to different strains of influenza virus and parvovirus will be described and the phylogeny/evolutionary trees constructed using the correlogram method will be compared, with the ones available in literature.

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