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dc.contributor.authorMahony, Shaun
dc.contributor.authorHendrix, David
dc.contributor.authorGolden, Aaron
dc.contributor.authorSmith, Terry
dc.date.accessioned2014-10-22T11:13:02Z
dc.date.available2014-10-22T11:13:02Z
dc.date.issued2005-05-01
dc.identifier.citationMahony, S., Hendrix, D., Golden, A., Smith, T.J., Rokhsar, D.S. (2005) 'Transcription factor binding site identification using the Self-Organizing Map'. BIOINFORMATICS, 1 (21(9)):1807-14.en_US
dc.identifier.issn1460-2059
dc.identifier.urihttp://hdl.handle.net/10379/4665
dc.descriptionJournal article (open access)en_US
dc.description.abstractMotivation: The automatic identification of over-represented motifs present in a collection of sequences continues to be a challenging problem in computational biology. In this paper, we propose a self-organizing map of position weight matrices as an alternative method for motif discovery. The advantage of this approach is that it can be used to simultaneously characterize every feature present in the dataset, thus lessening the chance that weaker signals will be missed. Features identified are ranked in terms of over-representation relative to a background model.Results: We present an implementation of this approach, named SOMBRERO (self-organizing map for biological regulatory element recognition and ordering), which is capable of discovering multiple distinct motifs present in a single dataset. Demonstrated here are the advantages of our approach on various datasets and SOMBRERO's improved performance over two popular motif-finding programs, MEME and AlignACE. SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero Contact: shaun.mahony@nuigalway.ieSupplementary information: http://bioinf.nuigalway.ie/sombrero/additionalen_US
dc.description.sponsorshipIRCSETen_US
dc.formatapplication/pdfen_US
dc.language.isoenen_US
dc.publisherOxford Open Journalsen_US
dc.relation.ispartofBIOINFORMATICSen
dc.titleTranscription factor binding site identification using the Self-Organizing Mapen_US
dc.typeArticleen_US
dc.date.updated2014-10-21T16:09:22Z
dc.local.publishedsourcehttp://dx.doi.org/10.1093/bioinformatics/bti256en_US
dc.description.peer-reviewedpeer-reviewed
dc.contributor.funder|~|
dc.internal.rssid1141111
dc.local.contactTerry Smith, School Of Natural Sciences, Nui Galway. 2022 Email: terry.smith@nuigalway.ie
dc.local.copyrightcheckedNo
dc.local.versionPUBLISHED
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