lncRNADetector – a bioinformatics pipeline for long noncoding RNA identification

Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs and potent regulatory elements in the living cells. High throughput RNA sequencing analyses have generated a tremendous amount of transcript sequence data. A large proportion of these transcript sequences does not code for proteins and are known as non-coding RNAs. Among them, lncRNAs are a unique class of transcripts longer than 200 nucleotides with diverse biological functions and regulatory mechanisms. Recent emerging studies and next generation sequencing technologies show a substantial amount of lncRNAs within the plant genome, which are yet to be identified. The computational identification of lncRNAs from these transcripts is a challenging task due to the involvement of a series of filtering steps.

Researchers from the CSIR-Central Institute of Medicinal and Aromatic Plants have developed lncRNADetector, a bioinformatics pipeline for the identification of novel lncRNAs, especially from medicinal and aromatic plant (MAP) species. The lncRNADetector has been utilized to analyze and identify more than 88,459 lncRNAs from 21 species of MAPs. To provide a knowledge resource for the plant research community towards elucidating the diversity of biological roles of lncRNAs, the information generated about MAP lncRNAs (post-filtering steps) through lncRNADetector has been stored and organized in MAPslnc database. The lncRNADetector web server and MAPslnc database have been developed in order to facilitate researchers for accurate identification of lncRNAs from the next generation sequencing data of different organisms for downstream studies.

Availability – The lncRNADetector web server and MAPslnc database are available at: https://lncrnapipe.cimap.res.in

Shukla B, Gupta S, Srivastava G, Sharma A, Shukla AK, Shasany AK. (2021) lncRNADetector: A Bioinformatics Pipeline for Long Non-Coding RNA Identification and MAPslnc: A Repository of Medicinal and Aromatic Plant lncRNAs. RNA Biol [Epub ahead of print]. [abstract]

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