:: DESCRIPTION

Phaistos is a collection of tools for proteins structure prediction. It currently features the FB5DBN and TorusDBN models, which make it possible to sample protein structures compatible with a given amino acid and/or secondary structure sequence.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux

:: DOWNLOAD

 Phaistos

:: MORE INFORMATION

Citation:

Thomas Hamelryck mail, John T Kent, Anders Krogh
Sampling Realistic Protein Conformations Using Local Structural Bias
PLoS Comput Biol 2(9): e131. doi:10.1371/journal.pcbi.0020131

:: DESCRIPTION

Mocapy++ is a Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux

:: DOWNLOAD

 Mocapy++

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Mar 12;11:126. doi: 10.1186/1471-2105-11-126.
Mocapy++–a toolkit for inference and learning in dynamic Bayesian networks.
Paluszewski M, Hamelryck T.

:: DESCRIPTION

MoAn is a discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux

:: DOWNLOAD

 MoAn

:: MORE INFORMATION

Citation:

Valen, E., Winther, O., Sandelin, A. and Krogh, A.
Discovery of regulatory elements is dramatically improved by a discriminatory approach.
PLoS Computational Biology 5(11) 2009

:: DESCRIPTION

miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux
• Ruby
• MySQL / PostgreSQL

:: DOWNLOAD

 miRMaid

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jan 14;11:29. doi: 10.1186/1471-2105-11-29.
miRMaid: a unified programming interface for microRNA data resources.
Jacobsen A, Krogh A, Kauppinen S, Lindow M.

:: DESCRIPTION

MASTR performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux

:: DOWNLOAD

 MASTR

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
Lindgreen S, Gardner PP, Krogh A.

:: DESCRIPTION

GMD is an R package to assess the similarity between spatial distributions of read-based sequencing data such as ChIP-seq and RNA-seq. GMD calculates the optimal distance between pairs of normalized signal distributions, optionally sliding one distribution over the other to ‘align’ the distributions. GMD also provides graphical and downstream clustering tools.

::DEVELOPER

Xiaobei Zhao <xiaobei at binf.ku.dk>, Albin Sandelin@The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux/ MacOsX/ Windows
• R package

:: DOWNLOAD

 GMD

:: MORE INFORMATION

Citation:

Xiaobei Zhao and Albin Sandelin
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads
Bioinformatics (2012) 28 (8): 1164-1165.

:: DESCRIPTION

BayesMD is a flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. BayesMD can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities.

::DEVELOPER

Man-Hung Eric Tang , Ole Winther.@The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux/ MacOsX/ Windows
• Matlab

:: DOWNLOAD

  BayesMD

:: MORE INFORMATION

Citation:

J Comput Biol. 2008 Dec;15(10):1347-63. doi: 10.1089/cmb.2007.0176.
BayesMD: flexible biological modeling for motif discovery.
Tang MH, Krogh A, Winther O.

:: DESCRIPTION

BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein’s backbone.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux/ MacOsX/ Windows
• Python

:: DOWNLOAD

 BASILISK

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jun 5;11:306. doi: 10.1186/1471-2105-11-306.
Beyond rotamers: a generative, probabilistic model of side chains in proteins.
Harder T, Boomsma W, Paluszewski M, Frellsen J, Johansson KE, Hamelryck T.

:: DESCRIPTION

BARNACLE (BAyesian network model of RNA using Circular distributions and maximum Likelihood Estimation) is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux/ MacOsX/ Windows
• Python

:: DOWNLOAD

 BARNACLE

:: MORE INFORMATION

Citation:

Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, HamelryckT (2009)
A Probabilistic Model of RNA Conformational Space.
PLoS Comput Biol 5(6): e1000406.

:: DESCRIPTION

Asap is an open source framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

:: REQUIREMENTS

• Linux/ MacOsX
• Python

:: DOWNLOAD

 Asap

:: MORE INFORMATION

Citation:

Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A:
Asap: a framework for over-representation statistics for transcription factor binding sites.
PLoS ONE 2008, 3(2):e1623