RNAmutants

is a web server to perform mutational analysis for a given RNA sequence. Previous methods relied on exhaustively enumerating k-point mutant sequences and subsequently applying mfold or RNAfold, a procedure with run time exponential in k. In contrast, RNAmutants computes the minimum free energy structure and Boltzmann partition function for all k-point mutants, for 0 ≤ k ≤ K, with run time O(K2n3). RNAmutants is described in the paper
Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote. Efficient algorithms for probing the RNA mutation landscape. PLoS Computational Biology, (2008) in press.

LocalMove

 is a web server to compute 3-dimensionals cubic and face-centered cubic lattice fits for both RNA and protein. Various levels of granularity are supported: backbone and several coarse grain models (CA, C1',P, etc.). Since optimal on-lattice fit for the cubic lattice is NP-complete, LocalMove implements the Monte-Carlo with simulated annealing, with a variety of user-definable parameters. LocalMove web server produces animated movies of the folding procedure, and stores job IDs for future reference. The web server and algorithm are described in Y. Ponty, R. Istrate, E. Porcelli, P. Clote. LocalMove: Computing on-lattice fits for biopolymers. Nucleic Acids Res. (Web Server Issue) (2008).

RNAbor

 RNAbor is a web server to compute secondary structural neighbors of a given RNA structure. The algorithm is described in Boltzmann probability of RNA structural neighbors and riboswitch detection. , Eva Freyhult; Vincent Moulton; Peter Clote, Bioinformatics. 2007 Aug 15;23(16):2054-62. Epub 2007 Jun 14. Abstract, PDF The web server is described in
  • RNAbor: A web server for RNA structural neighbors. E. Freyhult, V. Moulton, P. Clote. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W305-9. Epub 2007 May 25.

    • DIAL

     DIAL is a web server for 3-dimensional RNA structural alignment (global and local) and for motif detection. DIAL (DIhedral ALignment) runs in time that is quadratic in input length by performing an alignment which accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity, (iii) nucleotide base-pairing similarity. The algorithm and web server are described in DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities , F. Ferre; Y. Ponty; W. A. Lorenz; Peter Clote Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W659-68. Epub 2007 Jun 13.
    Abstract , Full Text, PDF.

    transFold

    transFold is a web server for beta-barrel supersecondary structure prediction. Unlike other software which employ machine learning methods, transFold uses multi-tape S-attribute grammars to describe the space of all possible supersecondary structures, then applies dynamic programming to compute the global energy minimum structure. The algorithm, due to J. Waldispühl, is described in Predicting transmembrane beta-barrels and interstrand residue interactions from sequence, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Proteins 65(1):61-74 (2006). BibTeX entry The web server, implemented by J. Waldispühl, is described in transFold: a Web Server for predicting the structure and residue contacts of transmembrane beta-barrels, J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert, Nucleic Acids Res. 34(Web Server Issue):189-193 (2006). BibTeX entry

    Boltzmann Time Warping

     Boltzmann Time Warping is software to compute the (symmetric, pairwise, all-against-all) time warping distance for gene expression time series values between two data sets. The user uploads two tab-separated textfiles of gene expression time series data, and the web server computes the time warping distance as well as the Boltzmann pair probability in the optimal alignment. Boltzmann pair probabilities provide a measure of potential biological significance of aligned positions. The new algorithms are due to P. Clote and described in Symmetric time warping, Boltzmann pair probabilities and functional genomics , P. Clote, J. Straubhaar, J Math Biol. 53(1):135-61 (2006). BibTeX entry and the web server is described in BTW: A web server for Boltzmann time warping of gene expression time series, F. Ferre, P. Clote, Nucleic Acids Res. 34(Web Server issue):W482-5 (2006). BibTeX entry

    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.

    DiANNA: Diresidue amino acid neural network for cysteine oxidation state 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. The extension to a ternary classifier using Support Vector Machines (SVMs), due to F. Ferre, is described in DiANNA1.1webServer.pdf DiANNA 1.1: An extension of the DiANNA web server for ternary cysteine classification, F. Ferre, P. Clote, Nucleic Acids Res. 34(Web Server issue):W182-5 (2006). BibTeX entry

    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.