###
Energy of k-point mutants of RNA

RNAmutants is software to predict
the expected energy of k-point mutants of a given RNA sequence, and
as well to compute the k-superoptimal secondary
structure, or secondary structure whose free energy is a minimum over
all pointwise mutants of a given RNA involving at most k mutated sites.
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.

### Cysteine classification and disulfide bond connectivity

DiANNA is software to predict both
cysteine oxidation state and which half-cystines partner with which
other half-cystines in disulfide bonds. The neural net design and
implementation is due to F. Ferre and P. Clote, and is described in
the papers:

Disulfide connectivity prediction using secondary
structure information and diresidue frequencies ,
F. Ferre and P. Clote,

*Bioinformatics* 21(10):2336-2346 (2005),
and

DiANNA: a web server for disulfide connectivity prediction ,
F. Ferre, P. Clote,

*Nucleic Acids Research*,
Nucleic Acids Res. 2005 Jul 1;

**33**(Web Server issue):W230-232.

### RNA energy spectrum computation (density of states)

RNALOSS
is a web server to compute the number and relative density of states
of RNA Locally Optimal Secondary Structures. The underlying algorithm
runs in O(n

^{4}) time and O(n

^{3}) space, and computes
the (relative) density of states for the entire energy
spectrum for the Nussinov-Jacobson energy for RNA secondary structures
on an input RNA. The algorithm and webserver are described in

An efficient algorithm to compute the landscape of
locally optimal RNA secondary structures with respect to the
Nussinov-Jacobson energy model ,
P. Clote,

*Journal of
Computational Biology* * 12*(1) 2005 83--101, and

RNALOSS: A web server for RNA locally optimal secondary structures ,
P. Clote,

*Nucleic Acids Research*,
web server W1-W5 (2005).

### rna dinucleotide shuffle

Dishuffle is a web
interface to a local implementation of the Altschul-Erikson
dinucleotide shuffle algorithm, described in
"Significance of nucleotide sequence alignments: A method for random
sequence permutation that preserves dinucleotide and codon usage",
S.F. Altschul and B.W. Erikson,
Mol. Biol. Evol., 2(6):526--538, 1985. This algorithm was used
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 in

*RNA* 11(5):578-591 (2005).

### Refined global and local alignments

Boltzmann Alignment
performs a (local) Smith-Waterman alignment of two input proteins,
then calculates the Boltzmann probability of any two aligned residues,
or residue aligned with gap symbol. This idea was first published in
"Stochastic Pairwise Alignments",
U. Mueckstein, I. L. Hofacker, and P. F. Stadler,

*Bioinformatics* 18 (suppl) 2002,
though it was later independently discovered and implemented in
April 2003 by P. Clote.
See

"Biologically significant sequence alignments using
Boltzmann probabilities" by P. Clote.