SigStb Web Interface

SigStb: A program for discovering unusual folding regions (UFRs) in RNAs. The computer program SigStb is designed to calculate two scores, significant score (SIGSCR) and stability score (STBSCR) of local segments in a sequence. The two standardized scores are defined as

SIGSCR = (E - E_r)/std_r

STBSCR = (E - E_w)/std_w

where E is the lowest free energy computed from a given folded segment, E_r and std_r 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, E_w and std_w 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 or Tinoco energy rules. The program is based on the dynamic programming algorithm and implemented in Fortran 77 running on Unix.

• Instruction of SigStb
• An example of input file
• An example of input sequence data
• An example of script file for running SigStb
• An example of output files
• References
• Download SigStb and SegFold

• SigStb Server for online users

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January 16, 2003