SPInDel Workbench

SPInDel Workbench performs species identification by analyzing insertion/deletion (indel)-defined hypervariable regions to generate numeric fragment-length profiles for taxonomic discrimination across eukaryotes, prokaryotes, and viruses.

Key Features:

• Indel-based numeric profiling: Generates numeric profiles from fragment lengths of hypervariable regions characterized by multiple indel variants.
• Multiplex analysis: Performs multiplex analysis of variable-length sequences to derive composite numeric signatures for specimens.
• Domain-wide identification: Enables species discrimination across eukaryotes, prokaryotes, and viruses without requiring DNA sequencing.
• High discrimination power: Demonstrated discrimination of 93.3% of eukaryotic species across 18 taxonomic groups.
• Reference profile database: Provides access to nearly 1,800 numeric profiles, including 1,556 for eukaryotes, 105 for prokaryotes, and 130 for viruses.
• Analytical functions: Supports sequence alignment, selection of informative hypervariable regions, PCR primer design, and statistical validation of identification results.
• Alignment-independent identification: Complements conventional DNA barcoding by avoiding ambiguities introduced by indels and in many cases eliminating the need for sequence alignment (e.g., rRNA genes).
• Validated in processed samples: Applied to discrimination of 10 mammalian species in highly processed food products with mixed-species content.

Scientific Applications:

• Ecological and taxonomic studies: Discrimination of species within genera such as Ansonia and Leptobrachium (frogs) and Apogon (coral reef fishes).
• Food authentication: Detection and discrimination of mammalian species in highly processed food products with mixed-species content.
• Work with suboptimal samples: Applicable to degraded or suboptimal DNA samples where indels are informative.
• Integration with genotyping platforms: Compatible with high-throughput genotyping workflows for large-scale screening.
• Molecular ecology: Use in molecular ecology investigations requiring broad-spectrum species identification.

Methodology:

Multiplex analysis of variable-length sequences; derivation of numeric profiles from fragment lengths of indel-defined hypervariable regions; selection of informative hypervariable regions; PCR primer design; sequence alignment and statistical validation of identification results.