[Biopython] RNA Secondary structure

[Peter]

On Mon, Mar 22, 2010 at 9:27 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Sat, Mar 20, 2010 at 2:53 AM, Gregory Barendt
> <barendt at mail.med.upenn.edu> wrote:
>> Does anyone know of good libraries for looking at RNA secondary
>> structure? I'm looking for particular stem loops in particular locations
>> in lots (hundreds of thousands) of sequences.
>>
>> Right now, I'm pretty inelegantly parsing the .ct file generated by
>> UNAfold. I need to modify my search to be a little more flexible, so
>> I'd much rather use an existing tool than continue to reinvent the
>> wheel. Any advice would be greatly appreciated.
>>
>> Thanks,
>> Greg
>
> I think Kristian Rother was looking at RNA support in Biopython last
> year (CC'd).
>

Hi again Greg,

In case you are not also on the dev mailing list, you might be interested
to look at Kristian's code. If you could help out with testing/feedback that
would be great:
http://lists.open-bio.org/pipermail/biopython-dev/2010-March/007482.html

Peter