Literature DB >> 34432277

MicroRNA Databases and Tools.

Tharcísio Soares de Amorim1, Daniel Longhi Fernandes Pedro1, Alexandre Rossi Paschoal2.   

Abstract

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Bioinformatics; Data analysis; Databases; Mirtrons; Prediction; Repository; Resources; Target gene; Tools; miRNAs

Mesh:

Substances:

Year:  2022        PMID: 34432277     DOI: 10.1007/978-1-0716-1170-8_7

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  84 in total

Review 1.  Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.

Authors:  Alexandre Rossi Paschoal; Vinicius Maracaja-Coutinho; João Carlos Setubal; Zilá Luz Paulino Simões; Sergio Verjovski-Almeida; Alan Mitchell Durham
Journal:  RNA Biol       Date:  2012-03-01       Impact factor: 4.652

Review 2.  Noncoding RNAs Databases: Current Status and Trends.

Authors:  Vinicius Maracaja-Coutinho; Alexandre Rossi Paschoal; José Carlos Caris-Maldonado; Pedro Vinícius Borges; Almir José Ferreira; Alan Mitchell Durham
Journal:  Methods Mol Biol       Date:  2019

Review 3.  microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

Authors:  Nagendra Kumar Singh
Journal:  Interdiscip Sci       Date:  2016-03-28       Impact factor: 2.233

4.  TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants.

Authors:  Xuan Ma; Chunyan Liu; Lianfeng Gu; Beixin Mo; Xiaofeng Cao; Xuemei Chen
Journal:  Bioinformatics       Date:  2018-05-01       Impact factor: 6.937

5.  TAM 2.0: tool for MicroRNA set analysis.

Authors:  Jianwei Li; Xiaofen Han; Yanping Wan; Shan Zhang; Yingshu Zhao; Rui Fan; Qinghua Cui; Yuan Zhou
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

6.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.

Authors:  R C Lee; R L Feinbaum; V Ambros
Journal:  Cell       Date:  1993-12-03       Impact factor: 41.582

7.  Tools4miRs - one place to gather all the tools for miRNA analysis.

Authors:  Anna Lukasik; Maciej Wójcikowski; Piotr Zielenkiewicz
Journal:  Bioinformatics       Date:  2016-04-08       Impact factor: 6.937

8.  miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data.

Authors:  Abhinav Kaushik; Shradha Saraf; Sunil K Mukherjee; Dinesh Gupta
Journal:  PeerJ       Date:  2015-10-20       Impact factor: 2.984

9.  mirtronDB: a mirtron knowledge base.

Authors:  Bruno Henrique Ribeiro Da Fonseca; Douglas Silva Domingues; Alexandre Rossi Paschoal
Journal:  Bioinformatics       Date:  2019-10-01       Impact factor: 6.937

10.  miRBase: from microRNA sequences to function.

Authors:  Ana Kozomara; Maria Birgaoanu; Sam Griffiths-Jones
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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