10/2002-03/2007: Undergraduate studies in biology, with specialisation in biochemistry, neurobiology and bioinformatics, at the University of Würzburg, Germany 03/2006-03/2007: Diploma thesis at the Department of Bioinformatics, University of Würzburg, Germany 04/2007-present: Undergraduate studies in human medicine at the University of Würzburg, Germany 01/2011-present: Research Assistant at the Evidence Based Medicine and Clinical Economy Group, Department of Anaesthesia and Critical Care, University Hospital of Würzburg, Germany
Abstract: An increasing number of phylogenetic analyses are based on the internal transcribed spacer 2 (ITS2). They mainly use the fast evolving sequence for low-level analyses. When considering the highly conserved structure, the same marker could also be used for higher level phylogenies. Furthermore, structural features of the ITS2 allow distinguishing different species from each other. Despite its importance, the correct structure is only rarely found by standard RNA folding algorithms. To overcome this hindrance for a wider application of the ITS2, we have developed a homology modelling approach to predict the structure of RNA and present the results of modelling the ITS2 in the ITS2 Database. Here, we describe the database and the underlying algorithms which allowed us to predict the structure for 86 784 sequences, which is more than 55% of all GenBank entries concerning the ITS2. These are not equally distributed over all genera. There is a substantial amount of genera where the structure of nearly all sequences is predicted whereas for others no structure at all was found despite high sequence coverage. These genera might have evolved an ITS2 structure diverging from the standard one. The current version of the ITS2 Database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Abstract: he internal transcribed spacer 2 (ITS2) of the ribosomal gene repeat is an increasingly important phylogenetic marker whose RNA secondary structure is widely conserved across eukaryotic organisms. The ITS2 database aims to be a comprehensive resource on ITS2 sequence and secondary structure, based on direct thermodynamic as well as homology modelled RNA folds.
Results: (a) A rebuild of the original ITS2 database generation scripts applied to a current NCBI dataset reveal more than 60,000 ITS2 structures. This more than doubles the contents of the original database and triples it when including partial structures. (b) The end-user interface was rewritten, extended and now features user-defined homology modelling. (c) Other possible RNA structure discovery methods (namely suboptimal and shape folding) prove helpful but are not able to replace homology modelling. (d) A use case of the ITS2 database in conjunction with other tools developed at the department gave insight into molecular phylogenetic analysis with ITS2.
