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.
Keywords for this software
References in zbMATH (referenced in 8 articles )
Showing results 1 to 8 of 8.
- Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
- Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
- Zytnicki, Matthias; Gaspin, Christine; Schiex, Thomas: DARN! A weighted constraint solver for RNA motif localization (2008)
- Duchesne, Jean-Eudes; Giraud, Mathieu; El-Mabrouk, Nadia: Seed-based exclusion method for non-coding RNA gene search (2007)
- Liu, Chunmei; Song, Yinglei; Malmberg, Russell L.; Cai, Liming: Profiling and searching for RNA pseudoknot structures in genomes (2005)
- Mauri, Giancarlo; Pavesi, Giulio: Algorithms for pattern matching and discovery in RNA secondary structure (2005)
- Xu, Ying; Wang, Lusheng; Zhao, Hao; Li, Jianping: Exact matching of RNA secondary structure patterns (2005)
- Backofen, Rolf; Gilbert, David: Bioinformatics and constraints (2001)