RNAsc

is a web server that computes RNA secondary structure with user-input chemical/enzymatic probing data, especially Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) or inline-probing data. Unlike other methods, RNAsc computes the partition function and minimum energy structure by applying Boltzmann derived weights applied to every nucleotide position. See
Integrating chemical foot printing data into RNA secondary structure prediction, by K. Zarringhalam, M.M. Meyer, I. Dotu, J.H. Chuang, P.Clote. PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.

RNAiFold

is a web server that solves the RNA inverse folding problem, using constraint programming. Given a target RNA secondary structure, as well as optional nucleotide constraints, RNAiFold determines all (or a large number of) RNA sequences, whose minimum free energy structure is the target structure. See
RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design J.A. Garcia Martin, Peter Clote, Ivan Dotu. J Bioinform Comput Biol 11(2): 1350001, 2013

Expected5to3distance

is a web server that computes the expected distance between the 5' and 3' ends of the Boltzmann ensemble of all secondary structures for a given RNA sequence. See
Expected distance between terminal nucleotides of RNA secondary structures. P. Clote, Y. Ponty, J.-M. Steyaert. J Math Biol. 2012 Sep;65(3):581-99. Epub 2011 Oct 9.

RNApagenumber

is a web server that computes the optimal "page number" of an RNA pseudoknotted or tertiary structure, input as a PDB file or .ct (mfold connect) file. See
On the Page Number of Secondary Structures with Pseudoknots. Peter Clote, Stefan Dobrev, Ivan Dotu, Evangelos Kranakis, Danny Krizanc, Jorge Urrutia. J Math Biol. 2012 Dec;65(6-7):1337-57. doi: 10.1007/s00285-011-0493-6.
where we show that computing the page number is NP-complete, and describe an approximation algorithm as well as an exact solution using constraint programming (CP). The web server is an implementation of the CP algorithm, which can compute the optimal page number for large RNAs within seconds -- for example the 23S chain PDB file 1FFK of length 2,922 for the Haloarcula marismortui ribosome.

RNAlocopt

is a web server that computes the partition function and samples structures from the ensemble of locally optimal secondary structures of a given RNA sequence. Here, a locally optimal secondary structure is one for which the free energy can not be lowered by the addition or removal of a single base pair (i.e. a kinetic trap in unit resolution energetics). The algorithm is described in the paper
Computing the partition function for kinetically trapped RNA secondary structures. W.A. Lorenz, P. Clote. Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178. doi:10.1371/journal.pone.0016178.

RNAborMEA

computes the maximum expected accurate δ-neighbors of a given RNA secondary structure for a given RNA sequence. Here, a structure T is a δ-neighbor of a given structure S, if S can be transformed into T by a minimum number δ of edit operations, where an edit operation consists of removing or adding a single base pair (i.e. if the base pair distance between S and T is δ). The algorithm is described in the paper
Peter Clote, Feng Lou, William A. Lorenz.
Maximum expected accuracy structural neighbors of an RNA secondary structure.
BMC Bioinformatics BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S.

RNA-WL

is an implementation of the Wang-Landau non-Boltzmannian sampling algorithm to approximate the partition function for RNA secondary structures. It is well-known that Monte-Carlo Boltzmannian sampling can be used to compute an approximation to the minimum free energy pseudoknotted structure for a given RNA sequence (allowing all possible pseudoknots). Since it is also NP-complete to compute the partition function for pseudoknotted RNA structures, Wang-Landau sampling can be used to estimate the density of states (from which the partition function can be computed). The algorithm is described in the paper
"Thermodynamics of RNA structures by Wang-Landau sampling." Feng Lou, Peter Clote. Bioinformatics 2010 Jun 15;26(12):278-86.

RNApathfinder

is a web server to compute near-optimal folding pathways between two given secondary structures for a given RNA sequence. Since this problem is known to be NP-complete, our main algorithm, RNAtabupath uses the TABU local search heuristic. The web server includes both downloadable source code for several algorithms, as well as a web engine to compute pathways. Intended applications concern folding pathways for RNA conformational switches. RNApathfinder and the RNAtabupath algorithm are described in the paper
I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote.
Nucleic Acids Res. 2010 Mar 1;38(5):1711-22.

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 Comput Biol. 2008 Aug 8;4(8):e1000124.

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.