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InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites.
Bioinformatics 2017 Februrary 16
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 https://www.jstacs.de/index.php/InMoDe .
Contact: [email protected].
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 https://www.jstacs.de/index.php/InMoDe .
Contact: [email protected].
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