[Bioperl-l] RNA fold

[Jason Stajich]

On Sat, 6 Dec 2003, Chris Fields wrote:

> I think, like the rest, that RNAFold may be the easiest way to go.
> mfold is a free program but distribution is bound up by licensing
> issues (I have it but can't redistribute it due to this; the web
> interfaces available have some limitations which I couldn't do
> without).  RNAFold doesn't have these problems and the source code is
> available on the web, plus (like Jason pointed out) there are perl
> interfaces.  There is also something in the book Genomic Perl on
> calculating energies and drawing secondary structures, but I haven't
> checked it out in detail.
>
> Personally, I am working on a bioperl parser for the RNAmotif program
> suite (used to search for conserved secondary structures based on a
> descriptor).  The rnamotif program is able to pass the motif hits to
> efn or efn2 for calculating free energy (based on different energy
> rules) and can output CT format files.  I'm also thinking about doing
> something similar for tRNAscan-SE and ERPIN at some point.  The problem
> I'm running into is how to store the secondary structure output for
> inclusion into GFF databases (I'm currently using
> Bio::SeqFeature::Generic for storing features).  Anyone?

Chris - I assume the structure is represented as string like
<<<...>>>> or ((((...)))) ?
If you do
$feat->add_tag_value('secondary_structure',$str);

This should store okay in a DB::GFF db or is that not really working for
you?


There are some newish bioperl objects Seq::Meta which are for representing
some bit of information about each base - maybe this is the place RNA or
Protein secondary structure information can be coded.
I'm not sure of what is best way to store these data - Heikki and others
have mostly worked on them so I can only hand wave at this point.


I'm not sure what type of computing you want to do on the data, depending
on what you want to do, might dictate creating/using different objects.
i.e. if you wanted to get the residues of the stems I think you might want
to build a special object which can represent the pairing after parsing it
out of the structure string.


-jason

>
> Chris Fields
> Postdoctoral Reseacher - Dept. of Biochemistry
> University of Illinois at Urbana-Champaign
>
> On Dec 5, 2003, at 2:22 PM, Vesko Baev wrote:
>
> > Hi to all,
> > if anyone knows a module or external program (which can be linked to
> > bioperl) for folding a RNA predicting hairpins and calculating a free
> > energy?
> >
> > Thanks to ALL!
> >
> > Vesselin Baev
> > Bulgaria
> >
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu