Structural Pattern Finder (SPF)

Our structural pattern finder is a tool that identify regions of a given RNA or DNA sequence that possess a high probability of being structured. This is achieved by computing, for each region, the difference between the folding free energy of the native sequence with the average folding free energy of randomized sequences of the same base composition.

The software employs the secondary structure prediction algorothm implemented in Pknots by Elena Rivas [1] and has been used to identify a structured region in mRNA involved in prion protein diseases[2].

The source code of the software is available and includes copies of the "squid"[3] library and of pknots[4]. Binaries for some computer architectures are provided. See the Readme file included for installation.

[1] E. Rivas and S.R. Eddy (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., (285) 2053-2068.

[2] I. Barrette, G. Poisson, P. Gendron and F. Major (2000) Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching, NAR, 2000.