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Nucleic Acids Research 2006 34(Web Server issue):W704-W707; doi:10.1093/nar/gkl129
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses

Jörg Schultz*, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar and Matthias Wolf*

Department of Bioinformatics, Biocenter, University of Würzburg Am Hubland, 97074 Würzburg, Germany

*To whom correspondence should be addressed. Jörg Schultz: Tel: +49 0931 888 4553; Fax: +49 0931 888 4552; Email: Joerg.Schultz{at}biozentrum.uni-wuerzburg.de and Matthias Wolf: Tel: +49 0931 888 4562; Fax: +49 0931 888 4552; Matthias.Wolf{at}biozentrum.uni-wuerzburg.de

Received February 13, 2006. Revised March 7, 2006. Accepted March 14, 2006.

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.


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