ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Programmed DNA elimination (PDE) is vital for germline-soma transitions in organisms from ciliates to nematodes.
• Existing software for detecting DNA splicing events, particularly PDEs, is limited.
• High-throughput sequencing data analysis requires efficient tools for identifying genomic alterations.

Purpose of the Study:

• To introduce Accurate Deletion Finder (ADFinder), a novel software for detecting programmed DNA elimination (PDE) events.
• To provide an efficient tool for analyzing high-throughput sequencing data to identify DNA splicing events.
• To facilitate downstream research and analysis of PDEs.

Main Methods:

• Development of Accurate Deletion Finder (ADFinder) software.
• Utilizing high-throughput sequencing data for PDE detection.
• Testing ADFinder on micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila.

Main Results:

• ADFinder effectively detects programmed DNA elimination (PDE) events using sequencing data.
• The software can predict PDEs even with low sequencing coverage.
• ADFinder identifies multiple alternative splicing forms and calculates their frequencies.

Conclusions:

• ADFinder is an effective tool for predicting large-scale PDEs.
• The software enhances the study of programmed DNA elimination and related genomic analyses.
• ADFinder is publicly available, promoting wider research application.