DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.
basic_science · Level V
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- Record sourced from PubMed, PMID 34524415.
- Also identified by DOI 10.1093/bioinformatics/btab624 and PMC identifier 8723152.
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Abstract
Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification. The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Bacteria
- Riboswitch