The rnamotif program  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.  and . An example of applying the code to finding tRNA genes is given in Ref. . The code was written by Tom Macke; Tom Macke and Dave Case wrote the Users' manual.
The Users' Manual (pdf format) is available here; it is also contained in the github repository referenced below.
 T. Macke, D. Ecker, R. Gutell, D. Gautheret, D.A. Case and R. Sampath. RNAMotif -- A new RNA secondary structure definition and discovery algorithm. Nucl. Acids Res. 29, 4724-4735 (2001).
 D. Gautheret, F. Major and R. Cedergren. Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. CABIOS 6, 325-311 (1990).
 A. Laferrière, D. Gautheret, and R. Cedergren. An RNA pattern matching program with enhanced performance and portability. CABIOS 10, 211-212 (1994).
 S.R. Eddy. RNABOB: a program to search for RNA secondary structure motifs in sequence databases. Unpublished.
 M.J. Serra, D.H. Turner, and S.M. Freier. Predicting thermodynamic properties of RNA. Meth. Enzymol. 259, 243-261 (1995).
 D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940 (1999).
 V. Tsui, T. Macke and D.A. Case. A novel method for finding tRNA genes. RNA 9, 507-517 (2003).
We thank Dave Ecker and Ranga Sampath for encouragement, and ISIS Pharmaceuticals for financial support; Robin Gutell and Daniel Gautheret for suggestions; Vickie Tsui for serving as a beta tester, and for many helpful comments and suggestions.
Version 3.1.1 (May, 2015) is available here:
RNAMotif is distributed under the terms of the GNU General Public License (GPL). See the README and COPYING.GNU files in the distribution for details. See the "revision.history" file for information on what has been changed with recent releases.