USING THE RNA SIMPLEX

For more information, including references to manuscripts and kinemage source, please read this.

If you have questions, please contact:

If the RNA Simplex or the accompanying data are used in further research, please cite:

• E. Schultes, P.T. Hraber and T.H. LaBean. 1997. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3:792-806.
• E. Schultes, P.T. Hraber and T.H. LaBean. 1999. A parameterization of RNA sequence space. Complexity 4:61-71.

To work with the RNA simplex, open KINEMAGE files with your copy of MAGE. It is best to use a large format monitor if possible. The simplex can be rotated in any direction using the mouse. Various data can be toggeled on and off using buttons on the right-hand side of the window. Clicking on specific data points will identify, in the lower left-hand corner of the window, the organismal source of the RNA sequence. Be sure to explore all the KINEMAGEs by choosing "next" from the KINEMAGE menu.

1. Start-up MAGE.5.01 and click on the PROCEED button.
2. Use the EXPAND button located in the upper right-hand corner of the graphics window to expand the size of the graphics window to maximum dimensions.
3. Use menu option, OPEN FILE, to open the "RNA Simplex.kin" data file.
4. The RNA simplex can be rotated by dragging the mouse. The ZOOM option is a sliding control feature located on the right-hand side of the graphics window. Other options can be found in the menu bar above the graphics window.
5. The buttons located along the right-hand side of the graphics window will display various data:
   • Tetrahedron: displays the boundaries of the RNA Simplex
   • Lines: these features display loci in composition space obeying the rule A=U&C=G (Chargaff's Axis, i.e., the gradient in G+C), A=G&C=U (gradient in G+A), or A=C&G=U (gradient in G+U). The compass feature displays a reference object at the isoheteropolymers and points in the directions to the homopolymers.
   • GA manifold: displays one of four order-disorder manifolds in RNA composition space. Sequences located on the manifold represent the most direct routes from the ordered region of sequence space (Chargaff's Axis) to disordered regions of sequence space (edges of the simplex other than the AU or CG edge). RNA sequence data are most closely associated with this manifold.
   • RNA: RNA composition data are listed as buttons by functional class and taxonomic descriptions.

• P, MF.A: mean base pairing propensity (P) of random sequences calculated using the mean-field approximation (MF.A.). The 1771 composition vectors spanning the simplex are arbitrarily divided into three groups from high to low mean base pairing propensity. This is the distribution of self-organization of RNA as a function of base composition.
• F, T.A.: mean frustration (F) of random sequences calculated using the thermodynamic approximation (T.A.). 100 random sequences from each composition vector were folded into secondary structures using computer algorithms. Displayed are the computed free energies averaged for each vector. The 1771 composition vectors spanning the simplex are arbitrarily divided into three groups from low to high mean frustration. This is the distribution of self-organization of RNA as a function of base composition.
• Entropy: displays all composition vectors in the simplex with Shannon entropy values between 1.3 and 1.5. The Shannon entropy has a minimum value of 0.0 at the homopolymers and a maximum value of 2.0 at the isoheteropolymers. Random walks in RNA sequence space will converge to high entropy composition vectors.
• M,F.A (0.64): evolutionary potential calculated using the mean-field approximation with m=0.64. Displayed are only the 1% most optimal composition vectors.
• T.A. (0.91): evolutionary potential calculated using the thermodynamic approximation with m=0.91. The 1771 composition vectors spanning the simplex are arbitrarily divided into four groups from high to low mean frustration.