Analyses of protein domains and genomic elements using bioinformatics approaches

Abstract

The main focus of the thesis is computational analysis of origin and evolution of genes based on the properties of the intron containing eukaryotic genes. It involved development of automated systems for extraction and integration of features from various sequence, structure and protein domain bio-databases. It also involved building interfaces for statistical analysis and visualization of features in large volume of data. Specifically, evolutionary significance of intron positions, intron phase combinations and intron conservation in eukaryotic protein homologues were studied. The correspondence of intron positions to the protein structural elements such as domains, secondary structures and modules in the genes that evolved before the divergence of the prokaryotes and eukaryotes were also performed. The statistical significance of these correspondences was then analyzed among taxonomic classifications in eukaryotes and intron phases to test various theories about intron and gene origin. The results supports mixed model for intron origin, which states that the present introns are mixture of the introns involved in exons shuffling of modules in the beginning of evolution and introns added in the later stage of evolution - during the metazoan development.