RNA Secondary Structures

[Laura Jaffe]

I am a graduate student in computer science working on
my master's thesis this summer.  My project is to objectively
compare various computer algorithms for determining
the secondary structure of RNA molecules. 

In order to evaluate the various algorithms, I am
collecting a large database of "known" RNA secondary
structures.  I have already located a source for
16S rRNA molecules.  I understand that the Berlin
Databank contains some 5S rRNA sequences, however
I do not know how to access this databank.  Any
help on accessing the Berlin Databank, as well as
additional sources of RNA sequences with known
secondary structures would be appreciated.

Also, I have implemented several folding algorithms
myself, and I would also like to include the
results on my database of any existing implementations 
of RNA folding algorithms.  If you know where I 
can obtain the source code for such implementations,
I would be very appreciative of your assistance.

Any additional comments or suggestions are welcome.

Laura Jaffe, tove at cs.umd.edu