Title page for ETD etd-02262011-120333


Type of Document Dissertation
Author Belal, Nahla Ahmed
Author's Email Address nbelal@vt.edu
URN etd-02262011-120333
Title Two Problems in Computational Genomics
Degree PhD
Department Computer Science
Advisory Committee
Advisor Name Title
Heath, Lenwood S. Committee Chair
Abdel-Hamid, Ayman Committee Member
Grene, Ruth Committee Member
Murali, T. M. Committee Member
Setubal, Joao Carlos Committee Member
Keywords
  • horizontal gene transfer
  • Two Problems in Computational Genomics
  • whole genome alignment
  • dynamic programming
  • Graph theory
  • biology and genetics
  • graph algorithms
  • partial order sets
Date of Defense 2011-02-14
Availability unrestricted
Abstract
This work addresses two novel problems in the field of computational genomics. The first is whole genome

alignment and the second is inferring horizontal gene transfer using posets. We define these two problems

and present algorithmic approaches for solving them. For the whole genome alignment, we define alignment

graphs for representing different evolutionary events, and define a scoring function for those graphs. The

problem defined is proven to be NP-complete. Two heuristics are presented to solve the problem, one is

a dynamic programming approach that is optimal for a class of sequences that we define in this work as

breakable arrangements. And, the other is a greedy approach that is not necessarily optimal, however, unlike

the dynamic programming approach, it allows for reversals. For inferring horizontal gene transfer, we define

partial order sets among species, with respect to different genes, and infer genes involved in horizontal gene

transfer by comparing posets for different genes. The posets are used to construct a tree for each gene.

Those trees are then compared and tested for contradiction, where contradictory trees correspond to genes

that are candidates of horizontal gene transfer.

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