ITSx

ITSx extracts ITS1, 5.8S, ITS2 and full-length ITS regions from ribosomal DNA sequences to enable accurate molecular barcoding, removal of non-ITS sequences, and improved downstream BLAST and clustering analyses for eukaryotic studies.

Key Features:

• Region extraction: Extracts ITS1, 5.8S, ITS2, and full-length ITS sequences from input ribosomal DNA sequences.
• Hidden Markov models (HMMs): Uses HMMs derived from extensive ribosomal gene alignments across diverse eukaryotic groups including fungi, metazoans, and plants to predict gene region boundaries.
• Sequencing support: Processes both Sanger and high-throughput sequencing datasets, including amplicon pyrosequencing.
• Scalability: Parallelizes processing to handle large datasets, demonstrated on datasets up to one million sequences.
• Accuracy: Achieves high true-positive extraction rates while minimizing false positives.
• Downstream sensitivity: Focuses analyses on ITS regions to increase sensitivity of BLAST searches and clustering operations.
• Noise reduction: Removes non-ITS sequences to reduce noise in diversity estimates from next-generation sequencing data.
• Implementation: Implemented in Perl.

Scientific Applications:

• Fungal taxonomy and identification: Enables extraction of ITS barcodes (ITS1/ITS2) used for species-level identification in fungi.
• Eukaryotic marker analyses: Supports ITS-based molecular studies across broader eukaryotic groups such as metazoans and plants.
• Environmental and amplicon studies: Processes large environmental amplicon datasets to improve diversity estimation and taxonomic profiling.
• Downstream sequence analysis: Improves sensitivity and precision of BLAST searches and clustering by providing ITS-focused sequences.

Methodology:

Implemented in Perl; employs hidden Markov models derived from ribosomal gene alignments to predict precise ITS1, 5.8S, ITS2 and full-length ITS positions and supports parallelized processing for large datasets.