The Computational Tools to Identify DNA Repeats and Motifs: A Systematic Review.

IF 2.9 4区医学 Q3 CHEMISTRY, MEDICINAL Current topics in medicinal chemistry Pub Date : 2024-11-21 DOI:10.2174/0115680266331305241113172257

Kavya Singh, Shreya Srivastava, Ashish Prabhu, Navjeet Kaur

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Abstract

Introduction: DNA repeats and motifs are specific nucleotide patterns/DNA sequences frequently present in the genomes of prokaryotes and eukaryotes. Computational identification of these discrete patterns is of considerable importance since they are associated with gene regulation, genomic instability, and genetic diversity and result in a variety of diseases/disorders.

Objective: In this article, the myriad of computational tools/algorithms and databases (~200 distinct resources) implicated in the detection of DNA repeats and motifs have been enlisted. This article will not only provide guidance to the users regarding the accuracy, reliability, and popularity (reflected by the citation index) of currently available tools but also enable them to select the best tool(s) to carry out a desired task.

Methods: The structured literature review, with its dependable and reproducible research process, allowed us to acquire 200 peer-reviewed publications from indexing databases, such as Scopus, ScienceDirect, Web of Science (WoS), PubMed, and EMBASE, by utilizing PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) regulations. Numerous keyword combinations regarding DNA repeats and motifs were used to create the query syntax.

Results: Initially, 3,233 research publications were retrieved, and 200 of them that satisfied the eligibility criteria for the detection and identification of DNA repeats and motifs by computational tools were chosen. A total of 200 research publications were recovered, of which 99 dealt with repeat prediction tools, 12 with repetitive sequence databases, 19 with specialized regulatory element databases, and 69 with motif prediction tools.

Conclusion: This article lists numerous databases and computational tools/algorithms (~ 200 different resources) that are involved in the identification of DNA repeats and motifs. It will help users choose the appropriate tool(s) for carrying out a particular task in addition to offering guidance on the reliability, dependability, and popularity (as indicated by the citation index) of currently available tools.

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识别 DNA 重复序列和基元的计算工具：系统综述》（The Computational Tools to Identify DNA Repeats and Motifs: A Systematic Review.

引言DNA 重复序列和图案是原核生物和真核生物基因组中经常出现的特定核苷酸模式/DNA 序列。计算识别这些离散模式相当重要，因为它们与基因调控、基因组不稳定性和遗传多样性有关，并导致多种疾病/失调：本文列举了与检测 DNA 重复序列和图案有关的大量计算工具/算法和数据库（约 200 种不同资源）。本文不仅将为用户提供有关当前可用工具的准确性、可靠性和流行度（通过引用指数反映）的指导，还将使他们能够选择最佳工具来完成所需的任务：结构化文献综述具有可靠、可重复的研究过程，我们利用 PRISMA（系统综述和元分析首选报告项）规定，从 Scopus、ScienceDirect、Web of Science (WoS)、PubMed 和 EMBASE 等索引数据库中获取了 200 篇同行评审出版物。在创建查询语法时使用了大量有关 DNA 重复序列和图案的关键词组合：初步检索了 3,233 篇研究论文，并选择了其中 200 篇符合通过计算工具检测和识别 DNA 重复序列和主题的资格标准的论文。共检索到 200 篇研究论文，其中 99 篇涉及重复预测工具，12 篇涉及重复序列数据库，19 篇涉及专门的调控元件数据库，69 篇涉及主题预测工具：本文列举了大量涉及 DNA 重复序列和主题的数据库和计算工具/算法（约 200 种不同资源）。除了就当前可用工具的可靠性、可信度和流行度（如引文索引所示）提供指导外，它还将帮助用户选择执行特定任务的适当工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Current topics in medicinal chemistry 医学-医药化学

CiteScore

6.40

自引率

2.90%

发文量

186

审稿时长

3-8 weeks

期刊介绍： Current Topics in Medicinal Chemistry is a forum for the review of areas of keen and topical interest to medicinal chemists and others in the allied disciplines. Each issue is solely devoted to a specific topic, containing six to nine reviews, which provide the reader a comprehensive survey of that area. A Guest Editor who is an expert in the topic under review, will assemble each issue. The scope of Current Topics in Medicinal Chemistry will cover all areas of medicinal chemistry, including current developments in rational drug design, synthetic chemistry, bioorganic chemistry, high-throughput screening, combinatorial chemistry, compound diversity measurements, drug absorption, drug distribution, metabolism, new and emerging drug targets, natural products, pharmacogenomics, and structure-activity relationships. Medicinal chemistry is a rapidly maturing discipline. The study of how structure and function are related is absolutely essential to understanding the molecular basis of life. Current Topics in Medicinal Chemistry aims to contribute to the growth of scientific knowledge and insight, and facilitate the discovery and development of new therapeutic agents to treat debilitating human disorders. The journal is essential for every medicinal chemist who wishes to be kept informed and up-to-date with the latest and most important advances.