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The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses
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 se...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538906/ https://www.ncbi.nlm.nih.gov/pubmed/16845103 http://dx.doi.org/10.1093/nar/gkl129 |
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author | Schultz, Jörg Müller, Tobias Achtziger, Marco Seibel, Philipp N. Dandekar, Thomas Wolf, Matthias |
author_facet | Schultz, Jörg Müller, Tobias Achtziger, Marco Seibel, Philipp N. Dandekar, Thomas Wolf, Matthias |
author_sort | Schultz, Jörg |
collection | PubMed |
description | 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 . |
format | Text |
id | pubmed-1538906 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-15389062006-08-18 The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses Schultz, Jörg Müller, Tobias Achtziger, Marco Seibel, Philipp N. Dandekar, Thomas Wolf, Matthias Nucleic Acids Res Article 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 . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538906/ /pubmed/16845103 http://dx.doi.org/10.1093/nar/gkl129 Text en © The Author 2006. Published by Oxford University Press. All rights reserved |
spellingShingle | Article Schultz, Jörg Müller, Tobias Achtziger, Marco Seibel, Philipp N. Dandekar, Thomas Wolf, Matthias The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title | The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title_full | The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title_fullStr | The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title_full_unstemmed | The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title_short | The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
title_sort | internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538906/ https://www.ncbi.nlm.nih.gov/pubmed/16845103 http://dx.doi.org/10.1093/nar/gkl129 |
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