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Pinkney HR, Wright BM, Diermeier SD. The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. Noncoding RNA. 2020;6(4)doi: 10.3390/ncrna6040049.
Pinkney, H. R., Wright, B. M., & Diermeier, S. D. (2020). The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. Non-coding RNA, 6(4), . https://doi.org/10.3390/ncrna6040049
Pinkney, Holly R, et al. "The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis." Non-coding RNA vol. 6,4 (2020). doi: https://doi.org/10.3390/ncrna6040049
Pinkney HR, Wright BM, Diermeier SD. The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. Noncoding RNA. 2020 Dec 16;6(4). doi: 10.3390/ncrna6040049. PMID: 33339309; PMCID: PMC7768357.
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Noncoding RNA. 2020 Dec 16;6(4). doi: 10.3390/ncrna6040049.

The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis.

Non-coding RNA

Holly R Pinkney, Brandon M Wright, Sarah D Diermeier

Affiliations

  1. Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand.

PMID: 33339309 PMCID: PMC7768357 DOI: 10.3390/ncrna6040049

Abstract

Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only a small subset of lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms of action by which new lncRNAs act, bioinformatic tools and databases are invaluable. Here, we review a selection of computational tools and databases for the in silico analysis of lncRNAs, including tissue-specific expression, protein coding potential, subcellular localization, structural conformation, and interaction partners. The assembled lncRNA toolkit is aimed primarily at experimental researchers as a useful starting point to guide wet-lab experiments, mainly containing multi-functional, user-friendly interfaces. With more and more new lncRNA analysis tools available, it will be essential to provide continuous updates and maintain the availability of key software in the future.

Keywords: RNA function; RNA interactions; RNA structure; bioinformatic prediction software; coding potential; computational analysis; databases; long non-coding RNAs; non-coding RNAs

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