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RASS server: RNA alignment in the joint sequence-structure space

  • RNA molecule A
  • PDB code or upload PDB file
    Chain ID
  • RNA molecule B
  • PDB code or upload PDB file
    Chain ID
  • Parameters
  • Structure A:
    Starting
    Ending

    Structure B:
    Starting
    Ending

    Lambda:


General description of functionality
Given 2 RNA chains, ESA will compute the geodesic distance between their three dimensional structures and/or sequences.
Input variables (labelled for RNA-A and RNA-B)
  • PDB code: PDB code containing an RNA chain. Can opt to specify the code or upload the PDB oneself.
  • Chain ID: Chain ID from the PDB file, which labels a RNA molecule.
Parameters
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 cross-validated 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.
P-value: Empirical significance of the geodesic distance with respect to a large number of RNA chains taken from the protein data bank. A small p-value 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 nucleotide-nucleotide global matching given by finding the correct re-parametrization 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.
Jinfeng Zhang, Ph.D.
Department of Statistics Florida State University
106E OSB 117 N. Woodward Ave. Tallahassee, FL 32306-4330
Tel: (850) 228-3897
Fax: (850) 644-5271
Email: jinfeng@stat.fsu.edu
Srivastava Ph.D.
Department of Statistics Florida State University
106D OSB, N. Woodward Ave. Tallahassee, FL 32306-4330
Phone: (850) 644-8832
Fax: (850) 644-5271
Email: anuj at stat.fsu.edu
Jose Laborde, PhD candidate
Department of Statistics Florida State University
201G, Oceanography and Statistics Bldg, FSU, Tallahassee, FL
Email: laborde@stat.fsu.edu
Gewen He, PhD candidate
Department of Computer Science Florida State University
102 Love Building 1017 Academic Way Tallahassee, Florida 32306
Tel: (850) 567-1001
Email: gh11c@my.fsu.edu
Programs can be downloaded at http://stat.fsu.edu/~jinfeng/ESA.html.