Tag: Motif Discovery

PRIORITY 2.1.0 – de novo Motif Discovery

PRIORITY 2.1.0

:: DESCRIPTION

PRIORITY is a tool for de novo motif discovery in the context of transcription factor (TF) binding sites. It implements a new approach to motif discovery in which informative priors over sequence positions are used to guide the search.

::DEVELOPER

Alex Hartemink

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  PRIORITY

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Jul 15;22(14):e384-92.
Informative priors based on transcription factor structural class improve de novo motif discovery.
Narlikar L, Gordan R, Ohler U, Hartemink AJ.

RNAprofile 2.2 – Secondary structure motif discovery in RNA sequences

RNAprofile 2.2

:: DESCRIPTION

RNAprofile is a software for the discovery of conserved sequence/structural motifs in unaligned RNA sequences

::DEVELOPER

the Pesolelab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RNAprofile

:: MORE INFORMATION

Citation:

Giulio Pavesi, Giancarlo Mauri, Marco Stefani and Graziano Pesole
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Nucl. Acids Res. (2004) 32 (10): 3258-3269.

GIMSAN 20100830 – Web-server tool for de novo Motif discovery

GIMSAN 20100830

:: DESCRIPTION

GIMSAN (GIbbsMarkov with Significance ANalysis) is a web-server tool for de novo motif discovery:

  • Hybrid Gibbs sampler for motif finding that uses a Bayesian prior on the percentage of sequences containing sites but uses a maximum likelihood approach on the motif matrix
  • Biologically realistic and reliable statistical significance analysis
  • Using a 3-Gamma approximation scheme
  • Factoring local sequence composition information
  • Reports an approximate 95% confidence interval of the point estimator of the motif p-value
  • Can be used to select the optimal width from a range of motif widths based on our significance analysis
  • Column pair dependency estimated using a Monte-Carlo scheme

GIMSAN Onlinr Version

:: DEVELOPER

Patrick Ng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GIMSAN

:: MORE INFORMATION

Citation:

Patrick Ng, Uri Keich.
GIMSAN: A Gibbs motif finder with significance analysis.
Bioinformatics, 24 (19): 2256-2257, 2008.

GADEM 1.3.1 – Motif Discovery tool for Large-scale Genomic Sequence data

GADEM 1.3.1

:: DESCRIPTION

GADEM is an unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.

::DEVELOPER

Leping Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GADEM

:: MORE INFORMATION

Citation:

Li L.
GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery.
J Comput Biol. 2009 Feb;16(2):317-29.

PriorsEditor 1.0.11 – Create and use Positional Priors in Motif Discovery

PriorsEditor 1.0.11

:: DESCRIPTION

PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true functional sites. Positional priors tracks can be constructed by manipulating, comparing and combining information about various features, including for instance phylogenetic conservation, DNase hypersensitive sites, repeat regions, nucleosome positions and other epigenetic data, physical properties of the DNA helix, distance from transcription start site or proximity to other known binding sites and many more. Data can be downloaded from the UCSC Genome Browser (or imported from file) and visualized with the graphical user interface. It is also possible to perform de novo motif discovery or motif scanning with known motif models by interfacing with locally installed programs. The results can then be visualized, analyzed and post-processed within PriorsEditor.

::DEVELOPER

Kjetil Klepper (kjetil.klepper@ntnu.no)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

PriorsEditor

:: MORE INFORMATION

Citation

Klepper, K. and Drabl?s, F. (2010)
“PriorsEditor: a tool for the creation and use of positional priors in motif discovery“.
Bioinformatics 26(17) : 2195-97