InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites
Ralf Eggeling1, Ivo Grosse2,3, Jan Grau2
1Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Helsinki, Finland.
Summary:
Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative higher order. The distinguishing feature of InMoDe is a robust model selection from a class of parsimonious models, taking into account dependencies only if justified by the data while choosing for simplicity otherwise.
Availability And Implementation:
InMoDe is implemented in Java and is available as command line application, as application with a graphical user-interface, and as an integration into Galaxy on the project website at http://www.jstacs.de/index.php/InMoDe .
Contact:
ralf.eggeling@cs.helsinki.fi.
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