Abstract

Previous studies have indicated that RNA play an important role in biological systems. The structures of local well-ordered folding sequences in RNA influence functions such as the control of replication, mRNA processing, metabolism and translation.

In this study the authors designed a procedure to calculate z-score of local segments in a sequence. The standardized z-score Zscr_e is defined as Zscr_e = (E_diff - E_diff(w))/std_w, where E_diff of a local segment is E_diff = E_f - E, E is the lowest free energy of the optimal structure folded by the segment, E_f is the optimal free energy when all base-pairs formed in the original optimal structure are prohibited, E_diff(w) and std_w are the mean and standard deviation. The authors supposed the measures Zscr_e and E_diff can denote the stability and uniqueness of the predicted RNA secondary structure from the local segment. The greater the Zscr_e and E_diff of the segment are, the more well-ordered the folded RNA structure is expected to be.

The program is based on dynamic programming algorithm and implemented in Fortran 90 on Unix. The source code of this program named ed.scan is available here: ftp://ftp.ncifcrf.gov/pub/users/shuyun/scan/ed.scan.tar.

References

1. Chen,S.-J. and Dill,K.A. (2000) RNA folding energy landscapes. Proc. Natl Acad. Sci. USA, 97, 646–651.

2. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol., 288, 911–940.

3. Zuker,M. and Jacobson,A.B. (1995) ‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucleic Acids Res., 23, 2791–2798.