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(n4) time and O(n3) 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.