[Bioperl-l] (RNAfold)Convert bracktes structure to aligned like tructure

Yousef Malik yousef at cs.haifa.ac.il
Sat Aug 21 19:22:10 EDT 2004


Hi
I would like to get your help on the following problem:
How could one convert the output of RNAfold within the brackets structure 
GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACAGUGCCGGCC
((((.((..((..((((.(((((..(((((((.(((((.......))..)))))))).)).))))).))))..))..)).)))) 
(-36.00)

To aligned like structure:
     A UG   AG    G     UU G     U   --  AC
GGCC G  UUG  AGGC GAGAC  G GCAAU GCU  GG  G
|||| |  |||  |||| |||||  | ||||| |||  ||  C
CCGG C  GAC  UCUG CUCUG  C CGUUA CGG  CC  U
     C GU   AG    G     UU A     -   GU  CG

Please reply to yousef at cs.haifa.ac.il
Reagrds
Malik



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