An updated overview and classification of bioinformatics tools for MicroRNA analysis, which one to choose?. (July 2021)

• Record Type: Journal Article
• Authors: Mortazavi, Sedigheh Sadat; Bahmanpour, Zahra; Daneshmandpour, Yousef; Roudbari, Faranak; Sheervalilou, Roghayeh; Kazeminasab, Somayeh; Emamalizadeh, Babak
• Is Part Of: Computers in biology and medicine. Volume 134(2021)
• Publication Date: 2021-07
• Subjects: miRNA -- Database -- Bioinformatics tools -- In silico; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2021.104544
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: The term 'MicroRNA' (miRNA) refers to a class of small endogenous non-coding RNAs (ncRNAs) regenerated from hairpin transcripts. Recent studies reveal miRNAs' regulatory involvement in essential biological processes through translational repression or mRNA degradation. Recently, there is a growing body of literature focusing on the importance of miRNAs and their functions. In this respect, several databases have been developed to manage the dispersed data produced. Therefore, it is necessary to know the parameters and characteristics of each database to benefit their data. Besides, selecting the correct database is of great importance to scientists who do not have enough experience in this field. A comprehensive classification along with an explanation of the information contained in each database leads to facilitating access to these resources. In this regard, we have classified relevant databases into several categories, including miRNA sequencing and annotation, validated/predicted miRNA targets, disease-related miRNA, SNP in miRNA sequence or target site, miRNA-related pathways, or gene ontology, and mRNA-miRNA interactions. Hence, this review introduces available miRNA databases and presents a convenient overview to inform researchers of different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant information rapidly. Highlights: Many Tools for miRNAs have been developed. Best is to combine miRNA tools results. In this review, miRNA-related online tools are classified.