Script Documentation (devel)

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Contents

 

Class LibVrna185

Encapsulates the Vienna Package version 1.8.5

 

LibVrna185.fold(sequence)

returns the Minimum Free Energy structure for the sequence passed as parameter.

 

LibVrna185.energyOfStruct(sequence, secstruct)

returns the free energy for the given sequence/secondray structure.

 

LibVrna185.foldWithConstraint(sequence, constraint)

returns the Minimum Free Energy structure for the sequence passed as parameter, with constraints applied

 

Example

 

var vrna = new LibVrna185;

var seq = 'CCCCGAAAGGGG';
var retval = vrna.fold( seq );
outln( seq );
outln( retval.mfe_structure );
outln( retval.free_energy );

delete vrna;

 

 

Class LibVrna211

Encapsulates the Vienna Package version 2.1.1

 

LibVrna211.fold(sequence)

returns the Minimum Free Energy structure for the sequence passed as parameter.

 

LibVrna211.energyOfStruct(sequence, secstruct)

returns the free energy for the given sequence/secondray structure.

 

LibVrna211.foldWithConstraint(sequence, constraint)

returns the Minimum Free Energy structure for the sequence passed as parameter, with constraints applied

 

Example

 

var vrna = new LibVrna211;

var seq = 'CCCCGAAAGGGG';
var retval = vrna.fold( seq );
outln( seq );
outln( retval.mfe_structure );
outln( retval.free_energy );

var constraint = '...x....x...';
retval = vrna.foldWithConstraint( seq, constraint );
outln( seq );
outln( constraint );
outln( retval.mfe_structure );
outln( retval.free_energy );

delete vrna;
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