Signature
func(s:seq, overlapping:bool=false, terminatorPredict:bool=false, windowSize:int=30, energyThreashold:real=-5.0,
symMapThreashold:real=10.0, loopSize:int=3, tweight:real=3.0, hybridEnergy:real=-11.7,
produceCTFile:bool=false -> any)
s:seq – the sequence (DNA
or RNA) for structure predictions
overlapping:bool – true for overlapping
structure prediction (default false)
terminatorPredict:bool – terminator prediction (default false)
windowSize:int – sliding window
size (default 30)
energyThreshold:real – energy threshold Kcal/mil (default –5)
symMapThreshold:real - symmetric mapping score threshold (default = 10)
loopSize:int -
initial hairpin loop size (default =3)
tweight:real - T
weight calculation (default = 3)
hybridEnergy:real - hybridization energy calculation
(default = -11.7)
A report in the
following format:
General prediction
>sequence name:
StrNo: start_site stop_site energy
Structure
Terminator
prediction
>sequence name:
StrNo: start_site stop_site energy T-weight
hybridization_energy
seq=upstream15nt/5stem loop 3stem /3downstream15nt
Structure
Wan, X.-F. and D.
Xu. Rnall: a new tool for local RNA secondary structure prediction. submitted.
Wan, X-F., and D.
Xu. Intrinsic terminator prediction and its application in
Synechococcus sp.
WH8102. submitted.