The webtool for prediction of mobility of bacterial plasmids and their potential hosts. The tool is very useful for a wide degree of research fields, which include analysis of development of antimicrobial resistance. The report that describes development of the tool is in publishing process.
F.11 Development of a new service
COBISS.SI-ID: 1539179972Lecture at the Seminar Computer and Information Science at the University FAMNIT, University of Primorska, where I presented the latest methods and results obtained with tools for prediction of structures of the DNA molecule, for analysis of regulatory regions in a variety of bacterial processes.
B.04 Guest lecture
COBISS.SI-ID: 1539180228Presentation at an annual symposium/meeting of a consortium of universities and experts in the field of analysis and prediction of structural properties of RNA and DNA molecules. Identification of regulatory regions in DNA is important for resolving biological processes. The representation of DNA molecules as strings of four letters, has in many cases been shown to be insufficient to describe protein binding features in regulatory regions and enable us to resolve the regions according to protein defined functional groups. A representation of DNA based on its conformational and physicochemical properties should therefore be tested and used in construction of algorithms for sorting and discovering regulatory regions. We applied our structural models and representations of DNA in a system of regions that regulate the transfer of bacterial plasmids. In this system, only about 60 such regions have been experimentally determined and sorted into 4 mobility groups defined by amino acid sequences of plasmid-encoded mobilization proteins. However, many more plasmids that carry such regulatory regions have been sequenced, and in light of the rising threat of antimicrobial resistance facilitated by horizontal gene transfer of plasmids, it is important to be able to quickly determine plasmid mobility by characterizing the regulatory regions. To facilitate characterization of regulatory regions and mobility groups, we developed bioinformatic procedures based on structural representations of DNA and a dynamic programming algorithm. The properties of the new representations and algorithm were tested and fine tuned using statistical procedures. Using the procedures, we discovered new regulatory regions in hundreds of plasmids and mobile elements. We statistically confirmed that DNA structural properties in regulatory regions are highly conserved in the mobility groups, much more in fact than nucleotide sequences. Therefore, the structural representation can be used to discriminate among the groups more efficiently than by using nucleotide sequences. Consequently, plasmid mobility groups can now be resolved with almost perfect accuracy, and procedures for prediction of plasmid MOB groups were implemented in a web-tool available at http://www.dnatools.eu.
B.06 Other
COBISS.SI-ID: 1539179716