InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites

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dc.contributor University of Helsinki, Helsinki Institute for Information Technology en
dc.contributor.author Eggeling, Ralf
dc.contributor.author Grosse, Ivo
dc.contributor.author Grau, Jan
dc.date.accessioned 2017-05-02T09:46:02Z
dc.date.available 2017-05-02T09:46:02Z
dc.date.issued 2017-02-15
dc.identifier.citation Eggeling , R , Grosse , I & Grau , J 2017 , ' InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites ' , Bioinformatics , vol. 33 , no. 4 , btw689 , pp. 580-582 . https://doi.org/10.1093/bioinformatics/btw689 en
dc.identifier.issn 1367-4803
dc.identifier.other PURE: 77673103
dc.identifier.other PURE UUID: 293c67f6-5465-4251-94fd-b520e7cc0c4d
dc.identifier.other WOS: 000397264100024
dc.identifier.other Scopus: 85028344582
dc.identifier.other ORCID: /0000-0002-3583-1029/work/32976126
dc.identifier.uri http://hdl.handle.net/10138/182241
dc.description.abstract 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. en
dc.format.extent 3
dc.language.iso eng
dc.relation.ispartof Bioinformatics
dc.rights en
dc.subject 113 Computer and information sciences en
dc.subject 112 Statistics and probability en
dc.subject 1182 Biochemistry, cell and molecular biology en
dc.title InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1093/bioinformatics/btw689
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
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