Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

By D. Gautheret, André Lambert. Journal of Molecular Biology, 2001

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In vivo genome editing using Staphylococcus aureus Cas9 (2015, methodology): “Rho-independent transcriptional termination was predicted using the ARNold terminator search tool 47,48 .”
Infernal 1.0: inference of RNA alignments (2009, background): “…and automatically construct an appropriate statistical scoring system that allows quantitative ranking of putative homologs in a sequence database (Gautheret and Lambert, 2001; grammars (SCFGs) provide a natural statistical framework for combining sequence and (non-pseudoknotted) secondary…”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, methodology): “However, the most generally useful approaches are those that take any RNA (or any multiple RNA alignment) as a query and use an appropriate scoring system to search a sequence database and rank highscoring similarities [10,11], just as programs like Blast (http:// www.”
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs (2013, methodology): “ERPIN [23] is a practical approach for the automatic derivation of an RNA signature from a sequence alignment and secondary structure, and finding the occurrence in sequence databases.”