+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

The ITS2 Database III--sequences and structures for phylogeny

The ITS2 Database III--sequences and structures for phylogeny

Nucleic Acids Research 38(Database Issue): D275

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.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 056190902

Download citation: RISBibTeXText

PMID: 19920122

DOI: 10.1093/nar/gkp966

Related references

Revisited ITS2 phylogeny of Anopheles (Anopheles) Hyrcanus group mosquitoes: reexamination of unidentified and misidentified ITS2 sequences. Parasitology Research 101(4): 885-894, 2007

Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept. Plos one 8(6): E66726, 2013

Phylogeny of genus Glossina according to ITS2 sequences. Science in China Series C Life Sciences 42(3): 249-258, 1999

The molecular phylogeny of the Miarus campanulae (Coleoptera: Curculionidae) species group inferred from CO1 and ITS2 sequences. Cladistics 22(3): 222-229, 2006

The placement of South African strains of Beauveria in a phylogeny inferred from rDNA ITS1-5.8S-ITS2 sequences. Journal of General and Applied Microbiology 57(5): 269-276, 2011

Characterization and phylogeny of Isaria spp. strains (Ascomycota: Hypocreales) using ITS1-5.8S-ITS2 and elongation factor 1-alpha sequences. Journal of Basic Microbiology 54(Suppl. 1): S21, 2014

Phylogeny of the Nasonia species complex (Hymenoptera: Pteromalidae) inferred from an internal transcribed spacer (ITS2) and 28S rDNA sequences. Insect Molecular Biology 2(4): 225-237, 1993

Comparative analysis of sequences and secondary structures of the rRNA internal transcribed spacer 2 (ITS2) in pollen beetles of the subfamily Meligethinae (Coleoptera, Nitidulidae): potential use of slippage-derived sequences in molecular systematics. Molecular Phylogenetics and Evolution 51(2): 215-226, 2009

First Molecular Identification and Phylogeny of Moroccan Anopheles sergentii (Diptera: Culicidae) Based on Second Internal Transcribed Spencer (ITS2) and Cytochrome c Oxidase I (COI) Sequences. Vector Borne and Zoonotic Diseases 18(9): 479-484, 2018

ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach. Gene 546(2): 145-149, 2014

Molecular morphometrics: Contribution of ITS2 sequences and predicted RNA secondary structures to octocoral systematics. Bulletin of Marine Science 81(3): 335-349, 2007

Molecular phylogeny of isolates of Ctenocephalides felis and related species based on analysis of ITS1, ITS2 and mitochondrial 16S rDNA sequences and random binding primers. Parasitology Research 94(3): 219-226, 2004

Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium. Fungal Genetics and Biology 46(11): 855-867, 2009

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Research 32(Database Issue): D593, 2004

Histone sequences database: Sequences, structures, post-translational modifications and genetic loci. Nucleic Acids Research 27(1): 323-324, 1999