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Analyzes nucleotide sequences for secondary structural motifs

  • David A. Case


Short Description

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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.



  • RNAmotif as well as other bioinfomatics programs can be found here with user manuals.


This is a command-line program, written in C. It should compile and run on most any platform.

User notes

Most computer will be able to run RNAmotif upon downloading, but some user may have to edit the 'config.h' file to customize the program for your settings.

  • Make sure your system is up to date, this seems to cause most of the problems.

See Also


[1] 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).

[2] 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).

[3] A. Laferriere, D. Gautheret, and R. Cedergren. An RNA pattern matching program with enhanced performance and portability. CABIOS 10, 211-212 (1994).

[4] S.R. Eddy. RNABOB: a program to search for RNA secondary structure motifs in sequence databases. Unpublished.

[5] M.J. Serra, D.H. Turner, and S.M. Freier. Predicting thermodynamic properties of RNA. Meth. Enzymol. 259, 243-261 (1995).

[6] 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).

[7] V. Tsui, T. Macke and D.A. Case. A novel method for finding tRNA genes. RNA 9, 507-517 (2003).

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