PHFinder

PHFinder detects point heteroplasmy in Sanger sequencing chromatograms by identifying double fluorescence peaks in chromatogram trace data to automate analysis of organellar genomes (mitochondrial and plastid DNA).

Key Features:

• Implementation: Implemented in Python to process chromatogram trace data.
• Automation: Automates identification of point heteroplasmies directly from Sanger sequencing chromatograms.
• Parameterization: Allows explicit specification of key parameters to infer double peaks indicative of heteroplasmy.
• Validation: In a validation study using Sanger sequencing data from 100 tissue samples of humpback whales (Megaptera novaeangliae), PHFinder detected 90% of known heteroplasmies.

Scientific Applications:

• Organellar genome analysis: Detection of heteroplasmy in mitochondrial and plastid DNA for studies of genetic variation.
• Evolutionary biology: Supports analyses of intra-individual and population-level mitochondrial variation in evolutionary studies.
• Population genetics and medical genetics: Applicable to population genetic surveys and studies of mitochondrial diseases.

Methodology:

Analyzes Sanger sequencing chromatogram trace data to infer double peaks indicative of point heteroplasmy using user-specified parameters; implemented in Python.