[Bioperl-l] secondary structure: AlignI ?

[Allen Day]

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).

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?

-Allen