DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.
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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 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.
SUBMITTER: Brewer KI
PROVIDER: S-EPMC8723152 | biostudies-literature |
REPOSITORIES: biostudies-literature
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