Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage
Related Experiment Video
Updated: Dec 17, 2025

Estimation of Telomeric Repeat-containing RNA from DNA/RNA Hybrid Complexes
Published on: December 5, 2025
Cong Feng1, Min Dai2, Yongjing Liu1
1Ming Chen's laboratory in Zhejiang University.
Abstract:
DNA repeats are abundant in eukaryotic genomes and have been proved to play a vital role in genome evolution and regulation. A large number of approaches have been proposed to identify various repeats in the genome. Some de novo repeat identification tools can efficiently generate sequence repetitive scores based on k-mer counting for repeat detection. However, we noticed that these tools can still be improved in terms of repetitive score calculation, sensitivity to segmental duplications and detection specificity. Therefore, here, we present a new computational approach named Repeat Locator (RepLoc), which is based on weighted k-mer coverage to quantify the genome sequence repetitiveness and locate the repetitive sequences. According to the repetitiveness map of the human genome generated by RepLoc, we found that there may be relationships between sequence repetitiveness and genome structures. A comprehensive benchmark shows that RepLoc is a more efficient k-mer counting based tool for de novo repeat detection. The RepLoc software is freely available at http://bis.zju.edu.cn/reploc.
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