Paper Info
Title
The ITS2 Database III--sequences and structures for phylogeny.
Abstract
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 (http://its2.bioapps.biozentrum.uni-wuerzburg.de) 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.
Year
DOI
Venue
2010
10.1093/nar/gkp966
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
internet,hidden markov model,web interface,computational biology
Biological classification,Annotation,Phylogenetic tree,Biology,Genetics,Phylogenetics,Hidden Markov model,GenBank,Taxon,Internal transcribed spacer,Database
Journal
Volume
Issue
ISSN
38
SUPnan
0305-1048
Citations 
PageRank 
References 
3
0.42
9
Authors
9
Name
Order
Citations
PageRank
Christian Koetschan130.42
Frank Förster294.31
Alexander Keller330.76
Tina Schleicher430.42
Benjamin Ruderisch591.35
Roland Schwarz61066.05
Tobias Müller7554.36
Matthias Wolf8556.39
Jörg Schultz912310.04