GimmeMotifs
http://131.174.221.43/bioinfo/gimmemotifs/index.htm
In the authors own words:
GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.
This package is simple to install on a Linux system via pre-compiled RPMs (Ubuntu/Debian/Fedora) or from source.
It includes a large number of popular motif discovery programs, including MDmodule, MEME, GADEM, MotifSampler, trawler, Improbizer, MoAn and BioProspector. Other motif finders, such as Weeder can be added via a simple config file.
Any combination of the available motif discovery programs can run and a consensus result is reported by clustering similar motifs from the different programs. Background sequences are derived from the user's input sequences. These take the form of random sequences sharing the same dinucleotide repeat frequencies, or real sequence from the same genome that share the same relative position to another random gene.
The main output is a clear HTML file that shows the motifs of interest along with an indication of the motif enrichment over the background sequences. The closest match between each significant discovered motif and the JASPAR database is also shown.
This tool provides a great first pass for large datasets, such as ChIP-seq data.
