# Rnall - local RNA secondary structure prediction

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)

##### Parameters

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)

##### Outputs

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

##### References

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.