ITS2 Database -- homology modelling RNA structure for molecular systematics

URL:
http://its2.bioapps.biozentrum.uni-wuerzburg.de/
What you can do:
Find information about phylogenetic marker ITS2.
Highlights:
  • The ITS2 Database holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank.
  • In the new version, Hidden Markov models (HMMs) are used for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline.
  • This allows 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.
Keywords:
  • internal transcribed spacer 2 (ITS2) prediction tool
  • internal transcribed spacer 2 secondary structure prediction tool
  • ITS2 phylogeny
  • rRNA phylogenetic markers
  • rRNA secondary structures
Literature & Tutorials:
PubMed Link: The internal transcribed spacer 2 databasex97a web server for (not only) low level phylogenetic analyses
-- 2008 Update: The ITS2 Database II: homology modelling RNA structure for molecular systematics
-- 2010 Update: The ITS2 Database III--sequences and structures for phylogeny
This record last updated: 02-03-2010
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