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

[Chris Fields]

I don't think there is a Bioperl module for  this, but I haven't looked for 
one extensively.  I think mfold can make output like this but I'm not sure 
if it can be done from paranthetical (Vienna RNAFold) format.

Chris

At 09:50 PM 8/21/2004, Yousef Malik wrote:

>  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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__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

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