Computational insights into intergenic regions and overlapping genes among prokaryote genomes

Identifier:  TDX:449

Handle: https://hdl.handle.net/20.500.11797/TDX449

Authors:  Pallejà Caro, Albert

Abstract:
Computational Insights into Intergenic Regions and Overlapping Genes among Prokaryote GenomesAlthough prokaryote organisms live in a huge variety of habitats, they have architectural features in common. In this thesis we analyze the intergenic regions and the overlaps between genes among the prokaryote genomes.Although the DNA compositional analysis brings us near to the origin of replication, alternative analyses are required in order to achieve better predictions. The overlaps between prokaryote genes tend to be short and they arise according to the structure of the genetic code. Furthermore, there is a selective pressure against the long ones. As longer is an overlap there is more risk of a deleterious mutation that can affect two proteins of the cell. We detected that the overlaps longer than 60 bps are due to sequencing or annotation errors. Regarding the intergenic regions we found that the presence of a regulatory signal such as the Shine-Dalgarno sequence (responsible of an efficient translation of the mRNA to protein) can influence the length of this regions and the stop codon usage of the previous genes. Finally, we developed the PairWise Neighbours database ( http://genomes.urv.cat/pwneigh/ ) which permits the study of the overlaps and its conservation across the species, as well as the SD presence within the intergenic regions.Albert Pallejà CaroDepartament de Bioquímica i BiotecnologiaUniversitat Rovira i VirgiliCampus Sesceladesc/Marcel·lí Domingo, s/n43007 Tarragona - Catalunya