Supplementary data for
"Complete RNA inverse folding: computational design
of functional hammerhead ribozymes",
by I. Dotu, J.A. Garcia-Martin, B.L. Slinger, V. Mechery,
M.M. Meyer, P. Clote.
Nucleic Acids Res. 2014 (in press).
Web Supplement

Supplementary data for
*Combinatorics of locally optimal RNA secondary structures*,
E. Fusy, P. Clote, *J Math Biol*.
Mathematica computations for asymptotics:
(1) asymptotics of external dangles ,
(2) asymptotics of UNAFOLD recursions .

Supplementary data
for benchmarking tests in article
"On Lattice Protein Structure Prediction Revisited", submitted by
Ivan Dotu, Manuel Cebrian, Pascal Van Hentenryck, Peter Clote to
IEEE Transactions on Computational Biology and Bioinformatics.

Python programs, Mathematica code, Maple session for
article "Combinatorics of Canonical and Saturated Secondary Structures"
by P. Clote, E. Kranakis, D. Krizanc and B. Salvy.
*J Bioinformatics and Computational Biology* (2009).

Python programs, Mathematica code for
article "Asymptotics of RNA shapes", by W.A. Lorenz, Y. Ponty and P. Clote,
*J Compu Biol* (2008).

Mathematica code, Maple code and pdf file of supplementary proof for
article "Asymptotics of RNA shapes", by W.A. Lorenz, Y. Ponty and P. Clote,
*J Compu Biol* (2008).

Data output by the software
RNAbor
for the collection of
SAM riboswitches retrieved from Rfam. The data
includes EMBL accession number, sequence, minimum free energy (mfe) secondary
structure predicted with RNAfold, number of k-neighbors for all k,
Boltzmann probability of k-neighbors from the mfe structure.
The software and applications are described in the article
Partition function for structural neighbors of
RNA with an application to riboswitch detection by
Eva Freyhult, Vince Moulton and Peter Clote,
Eva Freyhult; Vincent Moulton; Peter Clote,
Bioinformatics. 2007 Aug 15;23(16):2054-62. Epub 2007 Jun 14.

A
series of experiments on k-point mutants of RNA with the software
RNAmutants.
The algorithms are described in
Energy landscape of k-point mutants of an RNA molecule by
P. Clote, J. Waldispuhl, B. Behzadi, J.-M. Steyaert,
*Bioinformatics*, Vol. 21, 4140-4147, 2005.

Z-scores for Rfam :
List of Z-scores of minimum free energy for all Rfam classes, using
method described in the paper:
"Structural RNA has lower folding energy than
random RNA of the same dinucleotide frequency", by
P. Clote, F. Ferre, E. Kranakis, D. Krizanc,
*RNA*, **11**(5) (2005).