串联重复
串联
计算生物学
计算机科学
光学(聚焦)
生物
遗传学
基因组
基因
光学
物理
复合材料
材料科学
作者
Reza Behboodi,Mostafa Nouri-Baygi,Mahmoud Naghibzadeh
出处
期刊:BioSystems
[Elsevier]
日期:2023-04-01
卷期号:226: 104869-104869
被引量:4
标识
DOI:10.1016/j.biosystems.2023.104869
摘要
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.
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