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dc.contributor.authorKlepper, Kjetil
dc.contributor.authorDrabløs, Finn
dc.date.accessioned2015-09-21T11:59:02Z
dc.date.accessioned2015-12-03T12:48:10Z
dc.date.available2015-09-21T11:59:02Z
dc.date.available2015-12-03T12:48:10Z
dc.date.issued2013
dc.identifier.citationBMC Bioinformatics 2013, 14:9nb_NO
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11250/2366740
dc.description.abstractBackground: Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Results: Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. Conclusions: We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org.nb_NO
dc.language.isoengnb_NO
dc.publisherBioMed Centralnb_NO
dc.titleMotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysisnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewed
dc.date.updated2015-09-21T11:59:02Z
dc.source.journalBMC Bioinformaticsnb_NO
dc.identifier.doi10.1186/1471-2105-14-9
dc.identifier.cristin1022484
dc.description.localcode© 2013 Klepper and Drabløs; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.nb_NO


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