ADFinder

ADFinder detects programmed DNA elimination (PDE) events from high-throughput next-generation sequencing (NGS) data to enable analysis of germline-to-soma genomic transitions.

Key Features:

• Low Coverage Prediction: Predicts PDEs from relatively low sequencing coverage using NGS datasets.
• Detection of Multiple Splicing Forms: Identifies multiple alternative DNA splicing forms at the same genomic locus associated with PDEs.
• Frequency Calculation: Calculates the frequency of each detected splicing event to provide quantitative measures of prevalence.
• Genome-Wide Analysis Capability: Performs genome-wide DNA splicing event analysis and was validated on two micronuclear genomes, Oxytricha trifallax and Tetrahymena thermophila.

Scientific Applications:

• Genomic Transition Studies: Characterizing transitions between germline and somatic genomes by identifying PDE events.
• Evolutionary Biology Research: Investigating the role of PDEs in evolutionary processes across organisms ranging from unicellular ciliates like Oxytricha trifallax to multicellular nematodes.
• Functional Genomics: Exploring the functional implications of DNA splicing events on gene expression and regulation.

Methodology:

Leverages high-throughput NGS data and an algorithm designed to handle complex genomic datasets to identify and analyze subtle DNA sequence variations indicative of programmed eliminations, including operation on low-coverage data.