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

What's new

v3.0.13 (release 2011-05-30):

  • New database release containing 288044 structures

v3.0.5 (release 2010-11-08):

  • The last stable versions are now available on the webinterface!
  • database bugfix from release 3.0.4 (260923 structures)

v3.0.4 (release 2010-11-02):

  • database update (274310 structures). Old versions are available on request!

v3.0.3 (release 2010-05-01):

  • database update (234749 structures)

v3.0.2 (release 2009-12-15):

  • Added support for
    • Facebook
    • Twitter
    • RSS

v3.0.1 (release 2009-11-30):

  • New pseudoviewer visualization for complete structures

v3.0 (release 2009-09-29):

  • Overall redesign of database generation process
     
    • Accurate ITS2 HMM annotation
    • Exhaustive homology modeling
    • New dataset from NCBI - date: 22th June 2009
    • New estimated ITS2PAM50 matrix and gap-costs
    • Former database size nearly doubled
  • Motif
    Search for 3 major ITS2 motifs in Plants and Fungi
  • Model
    Enhanced custom modeling of multiple templates
  • Annotate
    Custom ITS2 HMM annotation
  • Blast
    Sequence and sequence/structure Blast

v2.6.3 (release 2009-08-06):

  • Motif scan for three ITS2 motifs works for plants and fungi

v2.6.2 (release 2009-07-29):

  • Added ITS2 highlight papers and press releases

v2.6.1 (release 2009-05-29):

  • Minor bugfix for Motif-Scan

v2.6 (release 2009-05-20):

  • Motif scan for three ITS2 motifs (Beta version works for plants)
  • New section: ITS2 of the month

v2.5.1 (release 2009-04-28):

  • New layout for Blast features

v2.5 (release 2009-04-15):

  • BLAST search for homologous sequences with known structure is now searching also for homologous sequences with unknown structures
  • BETA version of a sequence-structure BLAST

v2.4 (release 2009-03-18):

  • Included option to save sequence/structure for custom modeling and structure prediction
  • Mapped output of custom modeling into a synoptical table
  • Updated 'links' and 'cited by' pages
  • Included list of current ITS2 group publications

v2.3.1 (release 2009-02-10):

  • Minor bugfix for Annotation

v2.3 (release 2009-02-02):

  • Custom modeling now possible with multiple templates
  • Bugfix for saving images (PNG)

v2.2 (release 2009-01-25):

  • added a blast based homology search
  • added a flowchart for ITS2 based phylogenetic analyses

v2.1 (release 2008-10-21):

  • added HMM based ITS2 annotation
  • Database Updates working again. New update containing 111955 structure is online

v2.0.5 (release 2008-08-08):

  • added a number of citing articles
  • database update (note: currently our GeneMatcher II supercomputer for sequence alignment is out of order, therefore new homology modeled structures are not added to the database; remedy is on the way)

v2.0.4 (release 2007-10-17):

  • removed job offer (positions are filled)
  • variable gap penalties for the Custom Modeling service
  • wikipedia outlinks in lineages on the detail pages

v2.0.3 (release 2007-08-07):

  • added information on funding, usage policy and job offers
  • timestamps now displayed in a more readable manner

v2.0.2 (release 2007-07):

  • database update (added 4,507 full and 1,529 partial structures)
  • bugfix for annotation information in the details page
  • added new citations

v2.0.1 (release 2007-05):

  • Minor bugfixes (i.e. searching for GIs and Accession Numbers now works safely)
  • Regular taxonomy updates
  • SOAP web interface follows new database
  • added new citations

v2.0 (release 2007-01):

  • Rebuild and Redesign of Web Interface and Modeling Processes
     
    • new dataset from NCBI, usage of ITS2PAM50 matrix, BLAST reannotation facility, partial structures
    • original database size more than doubled, with partials nearly tripled
  • Details
    for each entry consisting of information on GI, Accession, insertion date, taxonomy lineage, sequence, structure, figure, free energy, structure discovery method, annotation method (original NCBI Nucleotide annotation, standard cutting, BLAST reannotation)
     
    • if the structure is a homology modeled structure: source sequence, full alignment, CBC and semi-CBC information, alignment E value, helix transfer percentages
    • if the structure is a model for other structures: a tree of structures modeled from currently viewed structure
    • if the structure is a partial structure: figure of template with homologous positions marked red
  • a Custom Modeling service
    template structures can be specified by the user or retrieved from the database
  • Database Statistics page
  • Latest Updates information
  • Browse and Search mode rewritten
  • Export to RNAStructML

v1.0 (release 2005-08)

If you use the database please cite.