DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria - PubMed (original) (raw)
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria
Kenneth I Brewer et al. Bioinformatics. 2022.
Abstract
Summary: 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.
Availability and implementation: 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 information: Supplementary data are available at Bioinformatics online.
© The Author(s) 2021. Published by Oxford University Press.
Figures
Fig. 1.
Overview of DIMPL. Process are divided into the two stages: genome analysis (A–E) and draft motif analysis (F–I). Annotations for sections D (Stav et al., 2019) and H (Rivas et al., 2017; Weinberg et al., 2011) have been reported previously
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