title: The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.
abstract: The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only recently, it became clear, that the ITS2 might be useful even for higher level systematic analyses. As the secondary structure is highly conserved within all eukaryotes it serves as a valuable template for the construction of highly reliable sequence-structure alignments, which build a fundament for subsequent analyses. Thus, any phylogenetic study using ITS2 has to consider both sequence and structure. We have integrated a homology based RNA structure prediction algorithm into a web server, which allows the detection and secondary structure prediction for ITS2 in any given sequence. Furthermore, the resource contains more than 25,000 pre-calculated secondary structures for the currently known ITS2 sequences. These can be taxonomically searched and browsed. Thus, our resource could become a starting point for ITS2-based phylogenetic analyses and is therefore complementary to databases of other phylogenetic markers, which focus on higher level analyses. The current version of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg Am Hubland, 97074 Würzburg, Germany. Joerg.Schultz@biozentrum.uni-wuerzburg.de
authors.forename: Jörg
authors.initials: J
authors.lastname: Schultz
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.forename: Marco
authors.initials: M
authors.lastname: Achtziger
authors.forename: Philipp N
authors.initials: PN
authors.lastname: Seibel
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Matthias
authors.initials: M
authors.lastname: Wolf
mesh_terms: D021903:DNA, Ribosomal Spacer / Q000737:chemistry* / Q000145:classification*; D030561:Databases, Nucleic Acid; D020407:Internet; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D021903:DNA, Ribosomal Spacer