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Updated: Jun 27, 2026

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

Published on: October 7, 2021

5.8S-28S rRNA interaction and HMM-based ITS2 annotation.

Alexander Keller¹, Tina Schleicher, Jörg Schultz

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

|November 26, 2008

Summary

Accurate delimitation of the internal transcribed spacer 2 (ITS2) is crucial for phylogenetic analysis. This study introduces a new hidden Markov model (HMM) tool to precisely identify and delineate ITS2 sequences, improving phylogenetic study reliability.

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The ITS2 Database

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Global Identification of Co-Translational Interaction Networks by Selective Ribosome Profiling

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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Molecular Biology
Bioinformatics
Phylogenetics

Background:

The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker due to its evolutionary rate and conserved secondary structure.
Inconsistent annotation of ITS2 start and end positions hinders accurate secondary structure prediction and phylogenetic analyses.
Correct ITS2 delineation is essential for reliable secondary structure modeling and multiple sequence alignments.

Purpose of the Study:

To develop and validate a novel tool for accurate ITS2 sequence delimitation and identification.
To address the shortcomings of existing methods in annotating ITS2 boundaries.
To provide a reliable method for the crucial initial step in ITS2-based phylogenetic studies.

Main Methods:

Utilized hidden Markov models (HMMs) for ITS2 identification and delimitation.
Verified annotations by comparing with conserved structural motifs in 5.8S/28S rRNA regions.
Applied the method to large datasets from GenBank and ITS2-DB for re-annotation.

Main Results:

Successfully identified and delimited ITS2 in over 30,000 unannotated GenBank entries.
Re-annotated approximately 45,000 questionable ITS2 sequences and 30,000 from ITS2-DB.
Demonstrated accurate annotation of ITS2 sequences ranging from 58 nt (Giardia lamblia) to 1160 nt (humans).

Conclusions:

The developed HMM-based tool provides accurate and reliable ITS2 delineation.
This method significantly improves the accuracy of phylogenetic analyses relying on ITS2 markers.
The tool is a valuable resource for researchers conducting molecular evolution and biodiversity studies.