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A Walkthrough to the Use of GreeNC: The Plant lncRNA Database

  • Andreu Paytuvi-Gallart
  • Walter Sanseverino
  • Riccardo Aiese CiglianoEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1933)

Abstract

Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time, and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and 6 algae, resulting in the annotation of more than 120,000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organized in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/). This chapter contains a detailed explanation of the content of GreeNC and how to access both programmatically and with a web browser.

Key words

lncRNAs Plants Annotation Pre-miRNA Folding energy lncRNAs database Plant lncRNAs database Database Repository 

Notes

Acknowledgments

We thank Dr. Antonio Hermoso Pulido from Centre for Genomic Regulation (CRG), who was also involved in the database development.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Andreu Paytuvi-Gallart
    • 1
  • Walter Sanseverino
    • 1
  • Riccardo Aiese Cigliano
    • 1
    Email author
  1. 1.Sequentia Biotech SLBarcelonaSpain

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