SegFold: A programs for discovering unusual folding regions (UFRs) in RNAs. The computer program SegFold is designed to calculate two scores, significant score (SIGSCR) and stability score (STBSCR) of local segments in a sequence by an extended search. In the extended search, the window size is systematically changed within a predetermined range (e.g., 40-350) in the potential interesting region which was previously detected by SigStb using a fixed-length window. The segment of minimal length and minimal scores of SIGSCR and/or STBSCR is selected as the region of potential interest. Consequently, UFRs in a sequence can be delimit precisely in the extended search. The two standardized scores are defined as
SIGSCR = (E - Er)/stdr
STBSCR = (E - Ew)/stdw
where E is the lowest free energy computed from a given folded segment, Er and stdr are the sample mean and sample standard deviation, respectively, of the lowest free energies from folding a large number of randomly shuffled sequences with the same size and base compositions as the given segment. Similarly, Ew and stdw are the sample mean and standard deviation of the lowest free energies obtained by folding all segments of the same size that are generated by taking successive, overlapping, fixed-length segments stepped one or several bases at a time along the sequence. The lowest free energies of formation of the folded segments are calculated by the dynamic programming algorithm with Turner energy rules. The program is based on the dynamic programming algorithm and implemented in Fortran 77 running on Unix.
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