EDscan is used to computer Z-scores, Zscre of the free energy difference, Ediff, between the lowest free energies of the optimized structure and its corresponding restrained structure in which the base-pairs in the optimized structure are prohibitted.
Ediff = Erestrained - Eoptimized
Zscre = ( Ediff - Ediff(w))/stdw
where Ediff(w) and stdw are the mean and standard deviation, respectively, of the Ediff scores computed by sliding a fixed-length window in steps of a few nucleotides from 5' to 3' along the searched sequence. The maximum sequence length is allowed upto 29995000 bp. In general the moving step size is 3-5 bp and window is less than 500 bp.
The program EDscan package (ed_scan.tar) includes following files:
1. Source Codes for EDscan:
formid.f gterg.f rna_ns.f, rna.inc, maxn.inc, and seq.inc scan.f 2. Energy Table Files for EDscan:
tnr.tbl (Turner energy rules for RNA folding) tnr_d.tbl (Energy parameters for DNA folding) It can be easily compiled by
f90 -o ed_scan -O3 -extend_source scan.f formid.f gterg.f rna_ns.f 3. A test job file: ed_scan.csh
4. An input sequence file: ed_scan.seq
5.An input control file: ed_scan.in
6. An output file: ed_scan.zscr