RNAMotif, an RNA secondary structure definition and search algorithm.

By T. Macke, D. Ecker, Robin Gutell, D. Gautheret, David A. Case, R. Sampath. Nucleic Acids Research, 2001

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ARNold: A web tool for the prediction of Rho-independent transcription terminators (2011, background): “Bacteria use two alternative mechanisms to terminate transcription: Rho-dependent termination involves the protein factor Rho and occurs at sites that cannot be easily characterized by their structure or sequence,(1) while Rho-independent termination involves sequence and structure signals that can ”
In vivo genome editing using Staphylococcus aureus Cas9 (2015, methodology): “Rho-independent transcriptional termination was predicted using the ARNold terminator search tool 47,48 .”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, methodology): “There are also pattern-matching algorithms that rely on expertly designed query patterns [9].”