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4.4 The ``Closed Excision'' option

This option is used to excise a portion of a structure that is either ``well-defined'' or for which a good secondary structure model already exists. The user is prompted by ``Enter beginning and end'', and should enter the historical numbers, i and j, for the base pair that closes off a structural motif that is to be excised. The program folds the remainder of the sequence, including the designated base pair. An example of a closed excision is given in Figure 3.

 FOLDING BASES    1 TO  290 OF ACJL                          
 ENERGY  =     -57.3
 
              10         20     
----GGC          -  G  T        
         CGGGCGCG GC GC CACGCCT-
         GTCCGCGC CG TG GTGCGGG-
AAAAAAA          G  G  -        
.      160       150        140 
 
                  170 
         TAA      AGC 
              TCCC   T
              AGGG   A
         ---      CTC 
                      
 
            180       190  
              GGC        | 
                 TGAGGCGGG-
                 ACTCTGCCC-
              ---        ^ 
                  280      

Figure 3: Printer output of the optimal folding of the Alu consensus sequence described in Figure 1. Closed excisions have been made at base pairs T²⁴-G¹⁴⁰ and G¹⁹¹-C²⁷⁵.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995