ABCC : Application's document Page

SigStb

RNA Analysis, Sequence Analysis, Bioinformatics

Shuyun Le, Bob Stephens and Jigui Shan
Advanced Biomedical Computing Center(ABCC)

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 - 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 or 
Tinoco energy rules. The program is based on the dynamic programming algorithm and 
implemented in Fortran 77 running on Unix.

IRIX64

/abcc/apps/`uname`/lecb/sigstb 

for web use:
http://www.abcc.ncifcrf.gov/app/htdocs/appdb/drawpage.php?appname=SigStb 
for commandline use:
./sigstb

http://protein3d.ncifcrf.gov/shuyun/sigstb.html

Bob Stephens
(301)846-5787
bobs@ncifcrf.gov

Jigui Shan
(301)846-5157
shanj@ncifcrf.gov

Jigui Shan and Bob Stephens