LocalMove – Compute On-lattice Fits for Biopolymers

LocalMove

:: DESCRIPTION

Local move is a Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Through a sequence of local moves, e.g. local backbone modifications, it walks through the conformational space, looking for a configuration as close as possible to the input 3D model, while keeping his points on-lattice. After a user-defined condition is triggered, the experiment stops and the currently best model can be retrieved as a PDB file.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W216-22. doi: 10.1093/nar/gkn367. Epub 2008 Jun 13.
LocalMove: computing on-lattice fits for biopolymers.
Ponty Y, Istrate R, Porcelli E, Clote P.

rnapagenumber – Compute Optimal “page number” of an RNA Structure

rnapagenumber

:: DESCRIPTION

rnapagenumber is a web server that computes the optimal “page number” of an RNA structure, input as a PDB file or .ct (mfold connect) file.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

On the page number of RNA secondary structures with pseudoknots.
P. Clote, S. Dobrev, I. Dotu, E. Kranakis. D. Krizanc, J. Urrutia,
J Math Biol. 2012 Dec;65(6-7):1337-57.

RNAbor – Compute Structural Neighbors of an RNA Secondary Structure

RNAbor

:: DESCRIPTION

RNAbor is a web server to compute secondary structural neighbors of a given RNA structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E. Freyhult, V. Moulton, P. Clote.
RNAbor: A web server for RNA structural neighbors.
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W305-9. Epub 2007 May 25.

DNAmelt r23 – Compute DNA Melting Properties

DNAmelt r23

:: DESCRIPTION

DNAmelt is a Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model.

::DEVELOPER

Tom Michoel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Matlab

:: DOWNLOAD

 DNAmelt

:: MORE INFORMATION

Citation:

Phys. Rev. E 73, 011908 (2006) [11 pages]
Helicoidal transfer matrix model for inhomogeneous DNA melting
Tom Michoel and Yves Van de Peer

SuperQ 1.1 – Compute a Phylogenetic Super Network

SuperQ 1.1

:: DESCRIPTION

SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 SuperQ

:: MORE INFORMATION

Citation

SuperQ: computing supernetworks from quartets.
Grünewald S, Spillner A, Bastkowski S, Bögershausen A, Moulton V.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):151-60. doi: 10.1109/TCBB.2013.8.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

DistMiss 1.0 – Compute Matrix of Genetic Distances between Populations

DistMiss 1.0

:: DESCRIPTION

DistMiss computes a matrix of genetic distances between populations on the basis of their allele frequencies at L loci.

::DEVELOPER

DistMiss Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Fortran

:: DOWNLOAD

 DistMiss

:: MORE INFORMATION

shustring 2.6 – Compute SHortest Unique SubSTRINGs

shustring 2.6

:: DESCRIPTION

shustring takes one or more sequences as input and returns the corresponding shustrings. The input data need to be in FASTA format, i.e. for each input sequence a definition line followed by the string(s) of residues. Input sequences can be over any alphabet.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

  shustring

:: MORE INFORMATION

Citation

Bernhard Haubold, Nora Pierstorff, Friedrich Möller and Thomas Wiehe
Genome comparison without alignment using shortest unique substrings
BMC Bioinformatics 2005, 6:123

rnalocopt 20101116 – Compute Partition Function of Locally Optimal RNA Secondary Structures

rnalocopt 20101116

:: DESCRIPTION

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).

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • WebServer
  • C Compiler

:: DOWNLOAD

 rnalocopt

:: MORE INFORMATION

Citation:

W.A. Lorenz, P. Clote.
Computing the partition function for kinetically trapped RNA secondary structures.
Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178.