AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Satellite DNA, characterized by low sequence complexity and poor mappability, presents significant challenges in genome assembly and analysis.
• Large heterochromatic arrays of tandem repeats are common in eukaryotic genomes but are often understudied.
• Existing methods for annotating tandem repeat arrays struggle with divergent or novel sequences.

Purpose of the Study:

• To introduce AniAnn's, an efficient algorithm for annotating large blocks of tandemly repeating DNA.
• To address the limitations of current methods in annotating satellite DNA and other tandem repeats.
• To provide a faster and more accurate approach for repeat annotation in diverse genomes.

Main Methods:

• AniAnn's leverages the high Average Nucleotide Identity (ANI) within repeat units of the same array.
• The algorithm rapidly infers the boundaries of large tandem repeat arrays.
• The approach was tested on various plant and animal genomes.

Main Results:

• AniAnn's demonstrates improved annotation of satellite and other tandem repeats across multiple species.
• The algorithm achieves high accuracy and speed, outperforming previous methods.
• AniAnn's requires a fraction of the runtime compared to existing approaches.

Conclusions:

• AniAnn's offers a robust solution for annotating challenging repetitive DNA regions.
• The software serves as a lightweight tool for repeat masking before whole-genome alignment.
• AniAnn's facilitates de novo annotation and classification of satellite repeats, advancing genomic research.