The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses
| Autor: | Jörg Schultz, Philipp N. Seibel, Marco Achtziger, Tobias Müller, Matthias Wolf, Thomas Dandekar |
|---|---|
| Rok vydání: | 2006 |
| Předmět: |
Internet
Web server Database Phylogenetic tree Sequence Analysis RNA Sequence analysis Biology computer.software_genre Article Homology (biology) User-Computer Interface Phylogenetics Rna structure prediction parasitic diseases DNA Ribosomal Spacer Genetics Nucleic Acid Conformation Internal transcribed spacer Databases Nucleic Acid Protein secondary structure computer Phylogeny Software |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only recently, it became clear, that the ITS2 might be useful even for higher level systematic analyses. As the secondary structure is highly conserved within all eukaryotes it serves as a valuable template for the construction of highly reliable sequence-structure alignments, which build a fundament for subsequent analyses. Thus, any phylogenetic study using ITS2 has to consider both sequence and structure. We have integrated a homology based RNA structure prediction algorithm into a web server, which allows the detection and secondary structure prediction for ITS2 in any given sequence. Furthermore, the resource contains more than 25,000 pre-calculated secondary structures for the currently known ITS2 sequences. These can be taxonomically searched and browsed. Thus, our resource could become a starting point for ITS2-based phylogenetic analyses and is therefore complementary to databases of other phylogenetic markers, which focus on higher level analyses. The current version of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|