The program SegFold is to explore a sequence by sliding a set of fixed-length windows consecutively along the sequence. The maximum sequence length is allowed upto 29995000 bp, and the maximum searching region is upto 10000 bp. In general, the searching region is a potential interesting region which was previously detected by SigStb using a fixed-length window. The size of searching region is often less than 600 bp, and window sizes are systematically changed in a step of 5-10 bp within 40-300 bp. In the new version, the random permutation is only performed in the extream cases where the empirical coefficients are not suitable to compute the means and standard deviation of the lowest free energies from a large sample of randomly shuffling sequences. Usually, the program does not need heavy computation.
The program SegFold package includes following files:
1. SegFold Source Codes: segfill.f msigfd.f segfold.f It can be easily compiled by f77 -col120 -vms_cc -O3 -static -o segfold segfold.f segfill.f msigfd.f 2. Energy Data Files for SegFold: turner.tbl (Turner energy rules for RNA folding) tinoco.tbl (Tinoco energy rules for RNA folding) ene.tbl, std.tbl ene2.tbl, and std2.tbl (Four files are used to computer sample mean and standard deviation, respectively, of the lowest free energies from randomly shuffled sequences based on the size and base compositions of the random sequences. The computed values are compatible with that computed from the random sequences directly by dynamic programming algorithm and Tinoco energy rules. cf20, cf30, cf50, cf100, and cf150 (Five files are used to computer sample mean and standard deviation, respectively, of the lowest free energies from randomly shuffled sequences based on the size and base compositions of the random sequences. The computed values are compatible with that computed from the random sequences directly by dynamic programming algorithm and Turner energy rules. 3. Test Data Files: Sequence file: segfold.seq Input control file: segfold.in Output files: segfold_d.sig segfold_d.stbl segfold_d.sigstbl