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Updated: Aug 8, 2025
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
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RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences.
Reza Behboudi1, Mostafa Nouri-Baygi1, Mahmoud Naghibzadeh1
1Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran.
Bio Systems
|March 1, 2023
Summary
The Rapid Perfect Tandem Repeat Finder (RPTRF) efficiently detects perfect tandem repeats in genomic sequences. This accurate and fast tool is accessible for global laboratory use, even with limited computing resources.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Tandem repeats are prevalent in eukaryotic genomes.
- These repeats influence cellular processes, disease association, and forensic applications.
Purpose of the Study:
- To develop an accurate, fast, and accessible tool for detecting perfect tandem repeats in genomic sequences.
- To address the need for a tool usable in diverse laboratory settings worldwide.
Main Methods:
- The Rapid Perfect Tandem Repeat Finder (RPTRF) utilizes file indexing to minimize character comparisons.
- An interval tree is employed in the filtering stage to accelerate output generation and prevent artifacts.
Main Results:
- RPTRF demonstrates high speed in identifying all perfect tandem repeats across various genomic sequences.
- The tool outperforms specialized imperfect tandem repeat detection tools on selected gold standards.
Conclusions:
- RPTRF provides an efficient and accessible solution for perfect tandem repeat detection.
- The tool's performance and usability make it valuable for genomic research and applications.
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