The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.

Area of Science:

• Molecular Biology
• Bioinformatics
• Phylogenetics

Background:

• The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker for generic and infrageneric classification due to its rapid sequence evolution.
• Recent findings suggest ITS2's utility in higher-level systematic analyses, leveraging its conserved secondary structure across eukaryotes.
• Reliable phylogenetic studies necessitate consideration of both ITS2 sequence and secondary structure information.

Purpose of the Study:

• To develop a computational resource for predicting internal transcribed spacer 2 (ITS2) secondary structures.
• To create a searchable database of pre-calculated ITS2 secondary structures for phylogenetic analyses.
• To provide a tool that integrates sequence and structure data for ITS2-based phylogenetics.

Main Methods:

• Integration of a homology-based RNA structure prediction algorithm into a web server.
• Development of a resource for detecting and predicting ITS2 secondary structures from input sequences.
• Population of the database with over 25,000 pre-calculated ITS2 secondary structures.

Main Results:

• A functional web server capable of predicting ITS2 secondary structures for any given sequence.
• A comprehensive database containing >25,000 pre-calculated ITS2 secondary structures, searchable by taxonomy.
• Establishment of a resource that combines sequence and structure data for ITS2 analysis.

Conclusions:

• The developed resource serves as a valuable starting point for ITS2-based phylogenetic studies, particularly at higher taxonomic levels.
• This tool complements existing databases for other phylogenetic markers by focusing on ITS2 sequence-structure relationships.
• The integration of secondary structure prediction enhances the reliability of ITS2 phylogenetic analyses.