The ITS2 Database III--sequences and structures for phylogeny

Nucleic Acids Res. 2010 Jan;38(Database issue):D275-9. doi: 10.1093/nar/gkp966. Epub 2009 Nov 17.


The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database ( which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160,000 correct full length and more than 50,000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Computational Biology / methods*
  • Computational Biology / trends
  • DNA, Ribosomal Spacer / genetics*
  • Databases, Genetic*
  • Databases, Nucleic Acid*
  • Fungi / genetics
  • Genome, Fungal
  • Genome, Plant
  • Information Storage and Retrieval / methods
  • Internet
  • Molecular Sequence Data
  • Plants / genetics*
  • Protein Structure, Tertiary
  • Sequence Homology, Nucleic Acid
  • Software


  • DNA, Ribosomal Spacer