public static HELM2Notation getSirnaNotation ( String senseSeq , String antiSenseSeq , String rnaDesignType ) throws NotationException , FastaFormatException , HELM2HandledException , RNAUtilsException , org . helm . notation2 . exception . NotationException , ChemistryException , CTKException , NucleotideLoadingException { HELM2Notation helm2notation = null ; if ( senseSeq != null && senseSeq . length ( ) > 0 ) { helm2notation = SequenceConverter . readRNA ( senseSeq ) ; } if ( antiSenseSeq != null && antiSenseSeq . length ( ) > 0 ) { PolymerNotation antisense = new PolymerNotation ( "RNA2" ) ; antisense = new PolymerNotation ( antisense . getPolymerID ( ) , FastaFormat . generateElementsforRNA ( antiSenseSeq , antisense . getPolymerID ( ) ) ) ; helm2notation . addPolymer ( antisense ) ; } validateSiRNADesign ( helm2notation . getListOfPolymers ( ) . get ( 0 ) , helm2notation . getListOfPolymers ( ) . get ( 1 ) , rnaDesignType ) ; helm2notation . getListOfConnections ( ) . addAll ( hybridization ( helm2notation . getListOfPolymers ( ) . get ( 0 ) , helm2notation . getListOfPolymers ( ) . get ( 1 ) , rnaDesignType ) ) ; ChangeObjects . addAnnotation ( new AnnotationNotation ( "RNA1{ss}|RNA2{as}" ) , 0 , helm2notation ) ; return helm2notation ; }
this method converts nucleotide sequences into HELM notation based on design pattern