Department of Statistics 
RASS server: RNA alignment in the joint sequencestructure space
Jose Laborde, Daniel Robinson, Anuj Srivastava, Eric Klassen and Jinfeng Zhang,
RNA global alignment in the joint sequencestructure space using Elastic Shape Analysis, Nucl. Acids Res. (2013) 41 (11): e114. doi: 10.1093/nar/gkt187
Wei Liu, Anuj Srivastava, Jinfeng Zhang.
A mathematical framework for protein structure comparison, PLoS Computational Biology 7(2), (2011): e1001075. doi:10.1371/journal.pcbi.1001075 General description of functionality
Given 2 RNA chains, ESA will compute the geodesic distance between their three dimensional structures and/or sequences.
Parameters Input variables (labelled for RNAA and RNAB)
Starting (for each structure A and B): Starting point from the piece of the chain that wants to be read.
Ending (for each structure A and B): Ending point from the piece of the chain that wants to be read. Note: Starting < Ending. Default is Starting = 1, Ending = 10000. Lambda: Weight for the nucleotide sequence. Values need to be greater or equal to zero. When zero is specified, the resulting geodesic distance takes into account only the structural shape difference but not the nucleotide sequences. When a large number (e.g. 70) is specified then the distance mainly takes into account the nucleotide sequence. However, recommended values for lambda should be between 0 and 10. The optimal crossvalidated value for lambda that optimizes classification of the FSCOR dataset is lambda = 5 (default). Output
Distance: Geodesic distance obtained from the Elastic Shape Analysis between both RNA chains.
Pvalue: Empirical significance of the geodesic distance with respect to a large number of RNA chains taken from the protein data bank. A small pvalue means that the distance is small enough to consider both chains related/similar in the structural sense. Geodesic Path: The geodesic paths are the shortest paths connecting the two RNA molecules in the shape space. The RNA backbones are viewed from 3 different angles in 3D. These views are slightly distorted by the the sequence weight. To view an undistorted version of the geodesic path choose lambda = 0 (i.e. use structure only for the comparison). Sequence alignment: The optimal nucleotidenucleotide global matching given by finding the correct reparametrization between their corresponding square root velocity functions (SRVFs). Structural Alignment: 3D optimal superposition with respect to the structures' center of gravity. Uses the optimal rotation from the ESA comparison.
Please contact Dr. Jinfeng Zhang for any questions.
Programs can be downloaded at http://stat.fsu.edu/~jinfeng/ESA.html.

