UPDATE AUGUST 2000: RNACAD software now available. Follow links from my homepage.

This server allows you to enter an RNA sequence and predict the secondary structure interactions interpreting the sequence as a bacterial small subunit ribosomal RNA. These results can then be used in analysis of secondary structure and to create multiple alignments.

A stochastic context free grammar(SCFG) is used to predict the secondary interactions. SCFG's are general modeling technique that can model a wide range of RNA structures. This grammar is a probabilistic model that has been trained to recognize bacterial small subunit ribosomal RNA.

This page can produce:

• a java viewer of your sequence's secondary structure.
• a secondary structure diagram of your sequence.
• an alignment of your sequence with E.coli.
• a list of all formed basepairs for your sequence.
• a multiple alignment of a set of sequences

Please see my homepage for links to descriptions of this work as well as the RNACAD software package that was used to create these results. The RNACAD package is a general RNA modeling package using stochastic context-free grammars.

Qualifications:

• Modeling RNA with a stochastic context free grammar disallows the modeling of of pseudoknotted interactions.
• The grammar is designed for full bacterial SSU rRNA sequences. If a non-bacterial SSU rRNA sequence is submitted then the grammar will try to interpret the sequence as bacterial as best it can. A prediction will be made but confidence in the results might not be high.
  
• If a segment of SSU rRNA sequence is submitted then the grammar will try to interpret the segment as the full sequence and will "spread" the segment across the grammar. The grammar performs a global rather than a local alignment.
• The Java secondary structure viewer requires a Java 1.1 compliant browser. See Netscape JDK for what Netscape currently provides.
• This server provides a very powerful model of RNA basepairing interactions and requires a large amount of both computer memory and time. Large numbers of prediction submissions are not encouraged. Please contact me, mpbrown@cse.ucsc.edu, if you would like to perform large scale experiments with this server. I would be more than happy to discuss running the experiments.

Thanks to the Ribosomal Database Project for rRNA alignments and secondary structure diagrams like the one on this page (originally created by Dr. Robin Gutell, University of Texas at Austin). B. L. Maidak, G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey and C. R. Woese. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-111 (1997)

Thanks to Michael Zuker for his program to display the secondary structure in postscript.
He helps maintain an energy based RNA folding server. This server folds RNA using a related method that utilizes thermodynamic information instead of base identity statistics.

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