Conference Paper

Novel Computational Methods for Large Scale Genome Comparison.

DOI: 10.1007/978-3-540-85861-4_9 Conference: 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, IWPACBB 2008, Salamanca, Spain, 22th-24th October 2008
Source: DBLP

ABSTRACT The current wealth of available genomic data provides an unprecedented opportunity to compare and contrast evolutionary histories
of closely and distantly related organisms. The focus of this dissertation is on developing novel algorithms and software
for efficient global and local comparison of multiple genomes and the application of these methods for a biologically relevant
case study. The thesis research is organized into three successive phases, specifically: (1) multiple genome alignment of
closely related species, (2) local multiple alignment of interspersed repeats, and finally, (3) a comparative genomics case
study of Neisseria. In Phase 1, we first develop an efficient algorithm and data structure for maximal unique match search in multiple genome
sequences. We implement these contributions in an interactive multiple genome comparison and alignment tool, M-GCAT, that
can efficiently construct multiple genome comparison frameworks in closely related species. In Phase 2, we present a novel
computational method for local multiple alignment of interspersed repeats. Our method for local alignment of interspersed
repeats features a novel method for gapped extensions of chained seed matches, joining global multiple alignment with a homology
test based on a hidden Markov model (HMM). In Phase 3, using the results from the previous two phases we perform a case study
of neisserial genomes by tracking the propagation of repeat sequence elements in attempt to understand why the important pathogens
of the neisserial group have sexual exchange of DNA by natural transformation. In conclusion, our global contributions in
this dissertation have focused on comparing and contrasting evolutionary histories of related organisms via multiple alignment
of genomes.

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