ITS2

ITS2 predicts ITS2 RNA secondary structures and provides a curated sequence-structure database to support phylogenetic and systematic analyses across eukaryotes.

Key Features:

• Homology-Based Structure Prediction: Predicts ITS2 secondary structures using conserved structural cores observed across diverse taxa to enable reliable sequence-structure alignments.
• Extensive Database: Contains over 25,000 pre-calculated ITS2 secondary structures corresponding to known ITS2 sequences.
• Structure-Aware Alignment: Supports automated alignment of highly divergent ITS2 sequences by integrating sequence and secondary-structure information.
• Hidden Markov Models (HMMs): Employs HMM-based annotation and delineation, yielding over 160,000 correct full-length and more than 50,000 partial ITS2 structures.
• Structure-Informed Similarity Search (modified BLAST): Uses a modified BLAST that incorporates sequence and secondary-structure information for improved similarity searches and taxon sampling.
• Motif Identification: Enables identification and searching of known and newly identified motifs within ITS2 sequences.

Scientific Applications:

• Species-level Phylogenetics: Combines ITS2 sequence and secondary-structure data to improve species-level resolution in phylogenetic analyses.
• Higher-level Systematics and Mega-systematics: Utilizes structural conservation to support phylogenetic inference across higher taxonomic ranks and large-scale systematic studies.
• Taxon Sampling and Novel Sequence Identification: Facilitates taxon sampling and annotation of novel ITS2 sequences via structure-aware similarity searches and HMM-based annotation.

Methodology:

Large-scale analysis of ITS2 sequences (>54,000 sequences) to validate a conserved structural core, homology-based RNA secondary-structure prediction, and an HMM-based annotation pipeline for identifying and modeling ITS2 structures.