[Bioperl-l] secondary structure: AlignI ?

[Jason Stajich]

You just need an extra 'track' for SimpleAlign objects which can hold the
representation of the secondary alignment string (per Q#6 -
http://www.sanger.ac.uk/Software/Rfam/help/gstart.shtml).

Would be good to have it added and then add the parsing/writing capability
to stockholm format as well per the format that Infernal expects.
ftp://ftp.genetics.wustl.edu/pub/eddy/software/infernal/Userguide.pdf


Peter had mentioned he wanted something in this vein as well during the
hackathon but I'm not sure if it ever got coded up?

-jason
On Thu, 31 Jul 2003, Allen Day wrote:

> What class would be best to use to start representing dna/rna secondary
> structure?  I have the output of a program called mfold
> (http://nar.oupjournals.org/cgi/content/abstract/31/13/3406) that i need
> to parse.
>
> I need to be able to align a sequence to itself, and for any aligned range
> be able to find it's partner's position.  The closest class to what I need
> is SimpleAlign, but it doesn't allow (as far as i can tell) a sequence to
> be aligned to itself.
>
> I ran into a related problem earlier in the week when I wanted to add many
> sequences containing more than one copy of a motif to an alignment (ie
> align multiple sections of the same sequence in an AlignI object).

You need to give them different names...
>
> Is it possible to do either of these with an existing class and I missed
> it?  If not should a new class be written, supporting AlignI interface,
> that can handle these cases?

Not sure - SimpleAlign is really for multiple sequence alignments
- if you want to identify positions of a motif to a single sequence I
think falls under a feature?

> -Allen
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu