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In this thesis we are concerned with constructing algorithms that address prob- lems of biological relevance. This activity is part of a broader interdisciplinary area called computational biology, or bioinformatics, that focuses on utiliz- ing the capacities of computers to gain knowledge from biological data. The majority of problems in computational biology relate to molecular or evolu- tionary biology, and focus on analyzing and comparing the genetic material of organisms. One deciding factor in shaping the area of computational biology is that DNA, RNA and proteins that are responsible for storing and utilizing the genetic material in an organism, can be described as strings over nite al- phabets. The. | n BRIC S Basic Research in Computer Science BRICS DS-00-4 C. N. S. Pedersen Algorithms in Computational Biology Algorithms in Computational Biology Christian N. S. Pedersen BRICS Dissertation Series DS-00-4 ISSN 1396-7002 March 2000 Copyright 2000 Christian N. S. Pedersen. BRICS Department of Computer Science University of Aarhus. All rights reserved. Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS Dissertation Series publications. Copies may be obtained by contacting BRICS Department of Computer Science University of Aarhus Ny Munkegade building 540 DK-8000 Aarhus C Denmark Telephone 45 8942 3360 Telefax 45 8942 3255 Internet BRICS@brics.dk BRICS publications are in general accessible through the World Wide Web and anonymous FTP through these URLs http www.brics.dk ftp ftp.brics.dk This document in subdirectory DS 00 4 Algorithms in Computational Biology Christian N0rgaard Storm Pedersen Ph.D. Dissertation Department of Computer Science University of Aarhus .
