motifanalysis 0.4.0 – Motif Analysis

motifanalysis 0.4.0

:: DESCRIPTION

motifanalysis allows the search of motifs with binding sites enriched in particular genomic regions.

::DEVELOPER

IZKF Computational Biology and Bioinformatics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 motifanalysis

:: MORE INFORMATION

RBPmap 1.0 – Motifs Analysis and Prediction of RNA Binding Proteins

RBPmap 1.0

:: DESCRIPTION

RBPmap is a computational tool that enables accurate prediction and mapping of RNA binding proteins (RBPs) binding sites on any RNA sequence or list of sequences of interest, provided by the users (as either sequences or genomic coordinates). RBPmap has been developed specifically for mapping RBPs in human, mouse and drosophila melanogaster genomes, though it supports mapping RBP binding sites in other organisms too.

::DEVELOPER

the Mandel-Gutfreund Lab, at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.
RBPmap: a web server for mapping binding sites of RNA-binding proteins.
Paz I, Kosti I, Ares M Jr, Cline M, Mandel-Gutfreund Y

motifGPU 1.0 – GPU-computing Accelerate Motif Analysis

motifGPU 1.0

:: DESCRIPTION

motifGPU is a library that uses GPUs to accelerate motif search. Extensive performance comparison studies on two different graphics cards from NVIDIA, (GeForce) GTX 260 and GeForce GTX 480, showed that commonly-used model-based motif scan procedures can be dramatically accelerated using our library. De novo motif discovery can also benefit from our GPU-accelerated tools.

::DEVELOPER

Steve Qin @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  motifGPU

:: MORE INFORMATION

For bug report, questions or comments, please contact Pooya Zandevakili (zandv@umich.edu).