MotifLab: A tools and data integration workbench for motif discovery and regulatory sequence analysis|
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
Discovering binding motifs and bindings sites for transcription factors is an important problem in bioinformatics, and many tools have been proposed to
search for novel motifs or to scan for potential sites that match established binding motifs. Unfortunately, traditional motif discovery and scanning methods
that only rely on sequence data have a tendency to make a lot of false predictions. However, it has been demonstrated that use of additional information,
such as gene expression, sequence conservation, location of DNase HS sites and epigenetic marks etc., has the potential to reduce the number of spurious
predictions and also discriminate between functional and non-functional binding sites. A lot of data that could prove useful for this purpose is already available at
genome-wide scales and more data for different organisms, cell-types and conditions is being published at an increasing rate.