Mashhad University of Medical Sciences, Faculty of Medicine, Department of Medical Biotechnology, Mashhad, Razavi Khorasan, Iran.
University of Tehran, College of Science, School of Biology, Department of Microbiology, Tehran, Tehran, Iran and Stem Cell Technology Research Center, Molecular Biology and Genetic Engineering Department, Tehran, Tehran, Iran.
Brief Bioinform. 2018 Mar 1;19(2):254-262. doi: 10.1093/bib/bbw109.
Recent discovery of thousands of small and large noncoding RNAs, in parallel to technical improvements enabling scientists to study the transcriptome in much higher depth, has resulted in massive data generation. This burst of information prompts the development of easily accessible resources for storage, retrieval and analysis of raw and processed data, and hundreds of Web-based tools dedicated to these tasks have been made available. However, the increasing number and diversity of bioinformatics tools, each covering a specific and specialized area, as well as their redundancies, represent potential sources of complication for end users. To overcome these issues, we are introducing an easy-to-follow classification of microRNA (miRNA)-related bioinformatics tools for biologists interested in studying this important class of small noncoding RNAs. We also developed our miRNA database miRNA algorithmic network database (miRandb) that is a meta-database, which presents a survey of > 180 Web-based miRNA databases. These include miRNA sequence, discovery, target prediction, target validation, expression and regulation, functions and their roles in diseases, interactions in cellular pathways and networks and deep sequencing. miRandb recapitulates the diverse possibilities and facilitates that access to the different categories of miRNA resources. Researchers can easily select the category of miRNA information and desired organism, in result eligible databases with their features are presented. This database introducing an easy-to-follow classification of available resources that can facilitate selection of appropriate resources for miRNA-related bioinformatics tools. Finally, we described current shortages and future necessities that assist researchers to use these tools easily. Our database is accessible at http://mirandb.ir.
最近发现了数千种大小不同的非编码 RNA，与此同时，技术的进步使得科学家能够更深入地研究转录组，从而产生了大量的数据。这些信息的爆发促使开发了易于访问的资源，用于存储、检索和分析原始和处理后的数据，并且已经提供了数百个专门用于这些任务的基于网络的工具。然而，生物信息学工具的数量和多样性不断增加，每个工具都涵盖了特定的和专业化的领域，以及它们的冗余，这代表了终端用户潜在的复杂化来源。为了克服这些问题，我们为有兴趣研究这种重要的小非编码 RNA 类的生物学家引入了一种易于遵循的 miRNA（microRNA）相关生物信息学工具分类法。我们还开发了我们的 miRNA 数据库 miRNA 算法网络数据库（miRandb），这是一个元数据库，提供了超过 180 个基于网络的 miRNA 数据库的调查。这些数据库包括 miRNA 序列、发现、靶标预测、靶标验证、表达和调控、功能及其在疾病中的作用、细胞途径和网络中的相互作用以及深度测序。miRandb 概括了不同的可能性，并方便访问不同类别的 miRNA 资源。研究人员可以轻松选择 miRNA 信息和所需生物体的类别，结果呈现出具有其特点的合格数据库。这个数据库引入了一种易于遵循的现有资源分类法，可以方便地选择与 miRNA 相关的生物信息学工具的适当资源。最后，我们描述了当前的短缺和未来的必要性，以帮助研究人员轻松使用这些工具。我们的数据库可在 http://mirandb.ir 上访问。
