Koetschan et al. (2010) NAR 38:D275-9
Selig et al. (2008) NAR 36:D377-380.
Schultz et al. (2006) NAR 34:W704-7.
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ITS2 3D structure
(Keller et al. 2010)


Chlorophyta hypertree

(Buchheim et al. 2011)
Fig1, Fig2, Fig3, Fig4

About

Optimal global pairwise alignments from about 270,000 ribosomal RNA (rRNA) internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures. Via 60,000 known ITS2 sequences that fit a common core of the ITS2 secondary structure described for the eukaryotes (Schultz et al. 2005), homology based modeling (Wolf et al. 2005) and reannotation procedures revealed in addition more than 150,000 homologous structures that could not be predicted by standard RNA folding programs.

Currently, there are 288044 structures available.

Contact:
Joerg.Schultz(at)biozentrum.uni-wuerzburg.de
Matthias.Wolf(at)biozentrum.uni-wuerzburg.de

Please cite:
The current version of the ITS2 database
Koetschan et al. (2010) NAR 38:D275-9.

The ITS2 Database can now also be accessed via a SOAP Interface.


4SALE
AUTOMATICALLY
GENERATES
SEQUENCE-STRUCTURE
ALIGNMENTS
 

The ITS2 Database III - sequences and structures for phylogeny

Koetschan et al. (2010) Nucleic Acids Research 38:D275-9

ITS2 Sequence-Structure Analysis in Phylogenetics: A How-to Manual for Molecular Systematics

Schultz, J., Wolf, M. (2009) Molecular Phylogenetics and Evolution 52(2): 520-3

5.8S-28S rRNA interaction and HMM-based ITS2 annotation   

Keller et al. (2009) Gene 430:50-7

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE   

Seibel et al. (2008) BMC Research Notes 1:91

ProfDistS: (Profile-) Distance based phylogeny on sequence - structure alignments

Wolf et al. (2008) Bioinformatics 24:2401-2

Distinguishing species

Müller et al. (2007) RNA 13:1469-1472

If you use the database please cite.