RepeatAnalyzer

RepeatAnalyzer analyzes short-sequence repeats (SSRs) and genotypes to track, catalog, and quantify SSR distribution and genetic diversity across prokaryotic and eukaryotic genomes, with validation on Anaplasma marginale.

Key Features:

• Tracking and Management: Catalogs short-sequence repeats (SSRs) and genotypes for systematic documentation of repeat sequences.
• Analysis Capabilities: Computes metrics assessing regional genetic diversity, SSR variety, and SSR regularity within loci.
• Visualization Tools: Generates geographic maps illustrating the distribution of genotypes and SSRs across regions of interest.
• Validation and Accuracy: Validated repeat identification and genotyping using 380 Anaplasma marginale isolates, confirming precision of repeat calls.
• Error Detection: Detects discrepancies in published data, including misreported SSRs, duplicate names for different SSRs, and multiple names assigned to a single SSR.

Scientific Applications:

• Genotype Identification: Uses heterogeneous SSR patterns within loci to assign strain genotypes for epidemiological and pathogen-evolution studies.
• Genetic Diversity Analysis: Quantifies regional genetic diversity to inform population structure and evolutionary dynamics.
• Data Correction and Validation: Identifies and helps correct errors in published SSR data to improve reliability of genomic datasets.

Methodology:

Employs novel metrics to evaluate SSR distribution, fits genotype-length distributions (reported as approximately normal) and SSR-frequency distributions (power-law-like), computes edit-distance distributions (identifying a common edit distance of five or six), and validates analyses using 380 Anaplasma marginale isolates; analyses report that over 90% of repeats are between 28 and 29 amino acids long.