USAT

USAT analyzes and visualizes tandem repeat (TR) haplotypes at single-nucleotide resolution to characterize alleles, compare haplotypes, and assess allele distribution for genetic, forensic, and diagnostic applications.

Key Features:

• Input processing: Processes TR haplotype outputs generated by existing bioinformatic tools.
• Allele size conversion: Converts allele sizes between sequence-based and length-based representations.
• Sequence-level comparison: Performs sequence comparison of TR haplotypes at single-nucleotide resolution.
• Comparative allele distribution: Analyzes and compares allele distribution across samples.
• Figure plotting: Generates plots and figures representing haplotype and allele comparisons.
• Interactive visualization: Provides interactive visualization capabilities for TR sequence and allele inspection.
• Parallel computing: Utilizes parallel computing to enable rapid processing of TR haplotype data.

Scientific Applications:

• Individual identification: Supports high-resolution allele and haplotype discrimination for individual identification.
• Forensic DNA profiling (CODIS): Applied to analysis and benchmarking of CODIS core STR loci in forensic investigations.
• Disease diagnostics: Facilitates characterization of tandem repeat variation relevant to disease-associated loci.
• Evolutionary and population genetics: Enables comparative studies of TR variation for evolutionary and population analyses.
• Benchmarking and comparative studies: Used to benchmark human individuals and compare TR haplotypes across datasets.

Methodology:

Processes TR haplotype outputs from other tools and performs allele size conversion, sequence-level haplotype comparison, figure plotting, comparative allele distribution analysis, and parallelized computation with interactive visualization.