Computer Science and Engineering, Department of


First Advisor

Peter Z. Revesz

Date of this Version


Document Type



A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Computer Science, Under the Supervision of Professor Peter Z. Revesz. Lincoln, Nebraska: December, 2003

Copyright (c) 2003 Viswanathan Ramanathan


DNA sequences are really huge having a length of around 3-4 million base pairs. Hence, each DNA sequence has to be cut down into small fragments using restriction enzymes. Once analyzed, these fragments have to be arranged or assembled into a single set of sequences called a genome map, to obtain the original DNA sequence. This problem is called the Genome Map Assembly Problem. A Constraint-Automata Solution was proposed for this purpose [11]. This thesis improves and implements the Constraint-Automata Solution to find all the possible solutions. The Modified Constraint-Automata Solution was implemented in Perl and executed on parts of various chromosomes of the human DNA. We show that the constraint automaton has a linear execution time.