Search Results for "motif"

We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. ...

CircularLogo is a light-weighted, easy to use web application that visualizes the intra-motif dependencies of a DNA or RNA motif.

...IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.

SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/

Maximal Clique Motif Reduction (MCMR) is a software program for running and then combining the output of multiple motif finder programs, such as MEME, AlignACE and Weeder, into a set of consensus predictions with associated confidence rankings.