Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Accurate annotation of the repeatome, including transposable elements, is essential for understanding genome evolution and function.
• Existing tools for repeat detection have limitations in sensitivity and speed, particularly for diverse repeat types.

Purpose of the Study:

• To develop a novel, sensitive, and efficient bioinformatics tool for genome-wide detection of various types of repeats and transposable elements.
• To improve the annotation of DNA and RNA transposable elements across plant and animal genomes.

Main Methods:

• Development of Generic Repeat Finder (GRF), a C++ program utilizing fast numerical algorithms and dynamic programming.
• GRF identifies terminal inverted repeats (TIRs), terminal direct repeats (TDRs), interspersed repeats, and associated transposable elements.
• Application of GRF to Arabidopsis, rice, and mouse genomes for repeat and miniature inverted-repeat transposable element (MITE) detection.

Main Results:

• GRF demonstrates high sensitivity in identifying TIRs, TDRs, interspersed repeats, and MITEs.
• GRF outperforms existing tools like detectIR, detectMITE, Inverted Repeat Finder, LTR_FINDER, and phRAIDER in speed and sensitivity for specific repeat types and genomes.
• GRF successfully detected various repeats and transposable elements in Arabidopsis, rice, and mouse.

Conclusions:

• GRF is a versatile and efficient tool for comprehensive repeatome annotation.
• The enhanced detection capabilities of GRF contribute to a deeper understanding of repeat element origins, biogenesis, and regulatory roles.
• GRF is an open-source tool, facilitating its adoption and further development in genomic research.