REPuter: the manifold applications of repeat analysis on a genomic scale

TLDR

Repetitive DNA in genomes holds many secrets, and systematic large‑scale study requires extensive algorithmic support. REPuter was designed as a fundamental tool for large‑scale repeat analysis, covering applications such as checking fragment assemblies, searching low‑copy repeats, finding unique sequences, comparing gene structures, and mapping cDNA/EST sequences. The program efficiently and completely detects various repeat types, evaluates their significance, and provides interactive visualization. The tool achieves efficient, complete repeat detection with significance evaluation and interactive visualization, demonstrating its utility across multiple sequence‑analysis applications.

Abstract

The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.