MrCaNaVaR

MrCaNaVaR analyzes NGS read-depth from sequence mappings to detect and predict absolute copy-number variations (CNVs), including segmental duplications and deletions, across genomic intervals.

Key Features:

• Copy Number Calling: Utilizes read depth from NGS sequence mappings to detect segmental duplications and deletions within genomic intervals.
• Absolute Copy Number Prediction: Predicts absolute copy numbers for specific genomic intervals, enabling precise quantification of CNVs rather than relative changes.
• Resolution of Duplicated Regions: Differentiates structure, copy number, and sequence content of nearly identical duplicated gene copies to distinguish individual copies.
• Comprehensive Read Mapping (mrFAST): Employs the mrFAST mapping algorithm to comprehensively map NGS reads, accounting for multiple mapping locations relevant to CNV detection.

Scientific Applications:

• Gene Innovation Studies: Maps and quantifies duplications to investigate how copy-number changes contribute to gene evolution and innovation.
• Phenotypic Variation Research: Detects genic copy-number differences associated with segmental duplications to study genetic contributions to phenotypic variability.
• Genomic Structural Analysis: Provides precise assessment of genomic content to distinguish highly identical gene copies for functional genomics and structural variation analyses.

Methodology:

MrCaNaVaR uses the mrFAST algorithm to comprehensively map NGS reads and performs read-depth analysis of sequence mappings to predict absolute copy-number variation.