The rnamotif program [1] searches a database for RNA sequences that match a ”motif” describing secondary structure interactions. A match means that the given sequence is capable of adopting the given secondary structure, but is not intended to be predictive. Matches can be ranked by applying scoring rules that may provide finer distinctions than just matching to a profile. The rnamotif program is a (significant) extension of earlier programs rnamot and rnabob [2-4]. The nearest-neighbor energies used in the scoring section are based on refs. [5] and [6]. An example of applying the code to finding tRNA genes is given in Ref. [7]. The code was written by Tom Macke; Tom Macke and Dave Case wrote the Users’ manual.

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