Computational tools for plant small RNA detection and categorization

@article{Morgado2019ComputationalTF,
  title={Computational tools for plant small RNA detection and categorization},
  author={Lionel Morgado and Frank Johannes},
  journal={Briefings in Bioinformatics},
  year={2019},
  volume={20},
  pages={1181 - 1192}
}
Abstract Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches… 

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References

SHOWING 1-10 OF 116 REFERENCES

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

A new software tool called PAREsnip is described that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments, to facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.

Criteria for Annotation of Plant MicroRNAs

The specific criteria required for the annotation of plant miRNAs are updated, including experimental and computational data, as well as refinements to standard nomenclature.

sRNAtoolbox: an integrated collection of small RNA research tools

Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

This work introduces an extension of the DARIO system to plant short non-coding RNAs (sncRNAs), which includes major modifications to cope with plant-specific sncRNA processing.

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

The UEA sRNA workbench is presented, a suite of tools that is a successor to the web-based UEE sRNA Toolkit, but in downloadable format and with several enhanced and additional features.

A toolkit for analysing large-scale plant small RNA datasets

A suite of web-based tools for processing plant small RNA datasets can be used to identify micro RNAs and their targets, compare expression levels in s RNA loci, and find putative trans-acting siRNA loci.

Learning sequence patterns of AGO-sRNA affinity from high-throughput sequencing libraries to improve in silico functional small RNA detection and classification in plants

Support vector machines on sRNA sequencing data obtained from AGO-immunoprecipitation experiments reveal that AGO affinity is strongly determined by complex k-mers in the 5’ and 3’ ends of sRNA, in addition to well-known features such as sRNA length and the base composition of the first nucleotide.

imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana

ImiRTP is presented, an integrated MTI prediction and analysis toolkit for Arabidopsis thaliana that features two important functions: combination of several effective plant miRNA target prediction methods provides a sufficiently large MTI candidate set, and different filters allow for an efficient selection of potential targets.

miRTour: Plant miRNA and target prediction tool

The bioinformatics pipeline miRTour is presented, which automates all the steps of miRNA similarity search, miRNA precursor selection, target prediction and annotation, each of them performed with the same set of input sequences.

A Review of Computational Tools in microRNA Discovery

Several commonly used tools in metazoan miRNA discovery are summarized, including prediction algorithms based on characteristics of miRNA molecules that have been developed to identify new miRNA species.
...