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

ITS2-Annotation

This sequence based tool uses HMMer (Eddy 1998) to annotate eukaryote "internal transcribed spacer 2" (ITS2) sequences with Hidden Markov Models (HMMs) (Keller et. al, Gene). It returns by definition of the ITS2 the sequence between the conserved 5.8S and 28S (or equivalent) rRNA (see Fig. 1). Therefore about 25 nucleotides of each ribosomal unit tailing the ITS2 are necessary for detection. For more information about HMMer visit the authors webpage. Further you may view statistics and supplementary materials: .

  • Choose a Model:
    Numbers in parenthesis represent number of sequences used for HMM modeling (starts and ends, respectively). Be aware that searches are more specific, effective and certain if a model different from "Eukaryotes" is chosen. This HMM is only suggested if other HMMs failed or taxonomic affiliation is unknown.
  • Maximum E-values:
  • Minimum size of ITS2:
  • Input your data in FASTA-format or provide a raw sequence.
  • Multiple sequences are allowed.
    E-value calculation is dependant of the amount of analyzed sequences (comparably to the size of a database). If you analyze multiple sequence it may help to increase the maximum E-value.
  • Names will be truncated to 50 characters (must be unique)
  • Analyze reverse complement (exclusively)
  • Include proximal stem in FASTA output
  • Example test sequences: Plants, Animals or Fungi.
    If you choose the plants examples, you will receive additional tooltip information for further analysis.

Fig. 1: Secondary structure of the internal transcribed spacer 2 (ITS2) with tailing parts of the 28S and 5.8S rRNA. This annotation tool searches for the end of the 5.8S and start of the 28S indicated by arrows (a and b, respectively). These parts are known to hybridize during ribogenesis before ITS2 cleavage.
Annotate!
Alternatively you may view the aligments of the Start HMM or the End HMM for the selected model.



If you use this tool, please refer to the ITS2-Database and remember to cite HMMer:
Eddy, S., 1998. Profile hidden Markov models. Bioinformatics 14, 755-763.

If you use the database please cite.