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Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
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Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

The ITS2 Database III--sequences and structures for phylogeny.

Christian Koetschan1, Frank Förster, Alexander Keller

  • 1Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland 97074 Wuerzburg, Germany.

Nucleic Acids Research
|November 19, 2009
PubMed
Summary
This summary is machine-generated.

The ITS2 Database now uses Hidden Markov Models for improved identification and annotation of RNA sequences, enhancing phylogenetic analyses. This resource aids in rapid taxon sampling and motif discovery for evolutionary studies.

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Last Updated: Jun 18, 2026

The ITS2 Database
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Published on: August 14, 2018

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • The internal transcribed spacer 2 (ITS2) is a crucial marker for phylogenetic studies.
  • Its conserved RNA structure is key to its utility.
  • Previous applications were primarily limited to species-level classification.

Purpose of the Study:

  • To enhance the ITS2 Database with advanced computational methods.
  • To expand the database's utility for broader phylogenetic applications.
  • To provide a comprehensive resource for sequence, structure, and taxonomic information of ITS2 markers.

Main Methods:

  • Development of a new annotation pipeline utilizing Hidden Markov Models (HMMs) for ITS2 identification.
  • Implementation of a modified BLAST search incorporating both sequence and structure information.
  • HMM-based annotation and modeling of novel sequences against multiple template structures.

Main Results:

  • Identification of over 160,000 full-length and 50,000 partial ITS2 structures.
  • Enhanced web interface enabling rapid taxon sampling via sequence-structure BLAST.
  • Capability to search for known and novel sequence motifs within the database.

Conclusions:

  • The redesigned ITS2 Database and web server offer a powerful, integrated resource for phylogenetic analyses.
  • The HMM-based approach significantly improves the accuracy and scope of ITS2 annotation.
  • The database facilitates deeper insights into evolutionary relationships across diverse taxa.