TaxMan

TaxMan trims reference small subunit ribosomal RNA (rRNA) gene sequences to primer-specific regions and evaluates primer specificity for amplicon sequencing of hypervariable regions to support taxonomic differentiation of bacterial communities.

Key Features:

• Primer-specific trimming: Accepts custom primer pairs and trims reference small subunit ribosomal RNA (rRNA) gene sequences to primer-targeted regions.
• Primer specificity assessment: Assesses primer coverage and specificity across taxa, identifying taxa that are amplified and taxa potentially missed by chosen primers.
• Reduced reference database size and computational acceleration: Trimming reduces the reference database size, lowering memory usage and yielding up to 98% faster run times for similarity searching (BLAST), chimera checking (UCHIME), and clustering (UCLUST).

Scientific Applications:

• Amplicon-based bacterial community profiling: Supports taxonomic assignment from amplicon sequencing of rRNA hypervariable regions to profile bacterial communities.
• Primer design and evaluation: Enables selection and evaluation of primer pairs based on taxonomic coverage of targeted hypervariable regions.
• Scalable processing of next-generation sequencing datasets: Reduces computational burden for large NGS datasets and downstream analyses such as BLAST, UCHIME, and UCLUST.

Methodology:

Researchers input primer sequences, TaxMan trims the reference rRNA database to those primer-targeted regions, and the trimmed sequences are used to assess primer specificity and accelerate sequence matching and downstream analyses.