A Review of Computational Tools in microRNA Discovery

Gomes, Clarissa P.C.; Cho, Ji-Hoon; Hood, Leroy; Franco, Octávio L.; Pereira, Rinaldo Wellerson; Wang, Kai

doi:10.3389/fgene.2013.00081

Cited by 92 publications

(63 citation statements)

References 103 publications

(124 reference statements)

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“…Many more tools have been developed for novel miRNA discovery and miRNA precursor prediction (htps://tools4mirs.org/software/ precursor_prediction/) [73] including frequently used tools like MiPred [79], miRanalyzer [75], miR-Abela [80], MiReNA [81], UEA sRNA Workbench [76] and mirDeep [74] ( Table 3). Major features of miRNA discovery tools have been reviewed [82][83][84]. Regarding livestock species, the choice of methods for miRNA discovery and novel miRNA annotation vary among studies and species.…”

Section: Tools For Mirna Identiicationmentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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Section: Tools For Mirna Identiicationmentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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“…14.2.3.1 -14.2.3.3 . Detailed reviews of RNA-seq data analyses of small RNAs have been published by Motameny et al ( 2010 ) and Gomes et al ( 2013 ).…”

Section: Specifi C Steps Of Rnaseq Data Analysis Of Small Rnasmentioning

confidence: 99%

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

Миронова

Weinholdt

Große

2014

Abiotic Stress Biology in Horticultural Plants

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Initiating the project on sequencing the Arabidopsis thaliana L . genome at the end of the twentieth century, researchers one day wished to expand the accumulated knowledge on Arabidopsis genetics to horticultural plants. The future arrived with the appearance of high-throughput sequencing technologies that allowed the investigation of transcriptomes of non-model plants at an unprecedented pace. RNA-seq experiments provide a unique opportunity of studying in depth the molecular-genetic basis for plant response to environmental cues. Here we substantiate the potential of RNA-seq experiments in applications to horticultural plants. The basic steps in RNA-seq data analysis and available software packages are presented in the fi rst section. Examples of RNA-seq data analyses, including studies of gene expression changes under various stresses in horticultural plants, and transcriptome analyses of the tolerance to abiotic stresses in horticultural plants are given in the second section.

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“…However, exorbitant price and requirements of highly specialized computational infrastructures and expertise still limit the large-scale application of this promising technology [23,24].…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Other Emerging miRNA Detection Strategies

Zhang

Dong

Tian

2015

SpringerBriefs in Molecular Science

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A number of specialized miRNA detection strategies have been recently reported, including surface plasmon resonance (SPR), microfluidic technique, next-generation sequencing, laser ablation (LA) inductively coupled plasma mass spectrometry (ICPMS), and so on. With a sensitive, rapid, and on-site analysis, SPR is an attractive alternative to conventional techniques in miRNA detection. Referring to small sample volume and rapid detection for POC diagnosis, microfluidic technique is a commendable choice. The possibility of new miRNA discovery is the major advantage of next-generation sequencing. And using LA-ICPMS for miRNA detection makes multiplexed, sensitive, and quantitative analysis possible with the sensitivity comparable to radioactive detection. For all these advantages, it is believed that in the future, these new technologies will emerge as an efficient and alternative tool for daily miRNA analysis.

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A Review of Computational Tools in microRNA Discovery

Cited by 92 publications

References 103 publications

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

Other Emerging miRNA Detection Strategies

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