RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences. (April 2023)

• Record Type: Journal Article
• Authors: Behboudi, Reza; Nouri-Baygi, Mostafa; Naghibzadeh, Mahmoud
• Is Part Of: Bio systems. Volume 226(2023)
• Publication Date: 2023-04
• Subjects: Consecutive tandem repeats -- Perfect tandem repeats -- Genomic sequences; Biological systems -- Periodicals; Biology -- Periodicals; Biology -- Periodicals; Evolution -- Periodicals; Biologie -- Périodiques; Évolution -- Périodiques; 570
• DOI: 10.1016/j.biosystems.2023.104869
• Languages: English
• ISSNs: 0303-2647

Abstract

Abstract: The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. The implemented tool and how to use it are available on GitHub .