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Secondary Structure Analyses
European Ribosomal Database
This site is no more maintained or updated. But its still the most valuable source for rRNA secondary structures on the net.
If you wonder what to do with those strange structure annotations of the ERDB, don´t worry. Just use the small script extractfromDCSE.exe from the
PHASE Package
It´ll convert the structures of the ERDB into the nice dot-bracket annotations.
Another useful site to get secondary structures of rRNA sequences is provided by Robin Gutell and therefore called
The Gutell Lab - Comparative RNA Web Site and Project
Not as many structures as on the ERDB, but fortunately provided in dot-bracket annotation.
Now, RNAsalsa analysis is done and you've got many many structure drawings in postscipt format, which actually do not look very nice. To work with RNAsalsa's structure drawings, you can use
which is a java based editor for playing with secondary structure drawings. It has many functions, some are very intuitive to find and learn, some are not ;-). Of course, XRNA needs a special input format, which can be generated by RNAplot. The latter is part of the notorious
Vienna RNA Package
Another editor for rRNA structure drawings is
which can handle the weird ERDB files.  
to be continued....