MAVisto (Motif Analysis and VISualisation TOolkit)is a tool for the exploration of motifs in network. It provides a flexible motif search algorithm and different views for the analysis and visualisation of network motifs.
p53scan is an algorithm to search for p53 consensus binding motif, as determined in a genome-wide ChIP-chip study, in DNA sequences. The same algorithm has also been combined with the p63 binding motif obtained from a genome-wide p63 ChIP-seq study in human keratinocytes to form p63scan.
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.
MUSA (Motif finding using an UnSupervised Approach) is a new algorithm that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders.
Solon P. Pissis, Alexandros Stamatakis, and Pavlos Pavlides.
MoTeX: a word-based HPC tool for MoTif eXtraction.
the Fourth ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2013), pp. 13-22, 2013. ACM Digital Library