3SEQ_2D

3SEQ_2D detects gene conversion events across whole genomes, identifying conversion tracts between paralogous genomic intervals to inform studies of genome evolution, ortholog identification, and functional annotation transfer.

Key Features:

• Detection of Gene Conversion Events: Identifies gene conversion events within paralogous pairs of genomic intervals by locating regions where one sequence has overwritten a highly similar sequence.
• Comprehensive Analysis: Analyzes large numbers of paralogous pairs (e.g., 1,616,329 pairs in the mouse genome) to detect conversion events at scale.
• Quantitative Insights: Quantifies gene conversion occurrence, detecting conversion events in approximately 7.5% of analyzed paralogous pairs.
• Detailed Property Analysis: Examines properties such as lengths of paralogous pairs and spatial relationships between source and target sequences.

Scientific Applications:

• Genome Evolution Studies: Enables analysis of gene conversion contributions to genome evolution by identifying conversion tracts and their properties.
• Ortholog Identification: Clarifies relationships among genomic intervals to improve accurate identification of orthologs across species.
• Functional Annotation Transfer: Informs transfer of functional annotations by accounting for sequence similarities caused by gene conversion rather than shared ancestry.

Methodology:

Pairwise comparisons of paralogous genomic intervals combined with statistical analyses to assess the likelihood that observed similarities reflect gene conversion; methodology exemplified by case studies on primate CCL gene clusters.