RepeatAround

RepeatAround identifies and analyzes direct, inverted, mirror, and complementary nucleotide repeats (3–64 bp) in circular genomes to characterize repeat distributions for mitochondrial DNA and comparative genomic studies.

Key Features:

• Repeat Identification: Locates direct, inverted, mirror, and complementary repeats and reports their genomic positions.
• Repeat Length Range: Detects repeats with lengths from 3 bp to 64 bp.
• Genome Scope: Operates on circular genomes and is applicable to mitochondrial DNA (mtDNA) analyses.
• Input Format: Accepts sequence input files in GenBank format.
• Multiple-Genome Comparison: Processes multiple genomes simultaneously to enable phylogenetic and comparative analyses.
• Visualization of Repeat Locations: Produces visual representations of repeat locations and indicates coding versus non-coding regions and proximity to specific genes.
• Output Spreadsheets: Exports detailed spreadsheets reporting the number and genomic coordinates of identified repeats for downstream analysis.
• Random Genome Generation: Generates randomized circular genomes (shuffled counterparts) to statistically evaluate observed repeat distributions.
• Motif Search: Searches for specific motifs and flanking sequences to confirm sequences around genomic rearrangements.

Scientific Applications:

• Human mtDNA Repeat Analysis: Applied to a large human mtDNA database to analyze Direct Repeat distribution across haplogroups and assess associations with macrodeletions.
• Comparative and Evolutionary Studies: Enables analysis of repeat patterns across species or populations for phylogenetic and evolutionary investigations.
• Rearrangement Validation: Uses motif searches to confirm flanking sequences around newly identified genomic rearrangements.

Methodology:

Detects direct, inverted, mirror, and complementary repeats (3–64 bp); parses GenBank files; processes multiple genomes simultaneously; generates randomized circular genomes by sequence shuffling for statistical evaluation; produces visual representations and spreadsheets; performs motif searches for flanking-sequence confirmation.