SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

Agostini, Federico, 1985-; Cirillo, Davide; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

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dc.contributor.author Agostini, Federico, 1985-ca
dc.contributor.author Cirillo, Davideca
dc.contributor.author Delli Ponti, Riccardo, 1987-ca
dc.contributor.author Tartaglia, Gian Gaetanoca
dc.date.accessioned 2015-12-14T14:51:01Z
dc.date.available 2015-12-14T14:51:01Z
dc.date.issued 2014ca
dc.description.abstract BACKGROUND: The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. RESULTS: Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment) algorithm for discovery of regulatory regions in nucleic acid sequences. SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences and (iii) an easy-to-use web-server interface. We applied our method to recently published data including 351 chromatin immunoprecipitation (ChIP) and 13 crosslinking immunoprecipitation (CLIP) experiments and compared our results with those of other well-established motif discovery tools. SeAMotE shows an average accuracy of 80% in finding discriminative motifs and outperforms other methods available in literature. CONCLUSIONS: /nSeAMotE is a fast, accurate and flexible algorithm for the identification of sequence patterns involved in protein-DNA and protein-RNA recognition. The server can be freely accessed at http://s.tartaglialab.com/new_submission/seamote.
dc.description.sponsorship The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013), through the European Research Council, under grant agreement RIBOMYLOME_309545, and from the Spanish Ministry of Economy and Competitiveness/n(SAF2011-26211). We also acknowledge support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012-0208)
dc.format.mimetype application/pdfca
dc.identifier.citation Agostini F, Cirillo D, Ponti RD, Tartaglia GG. SeAMotE: a method for/nhigh-throughput motif discovery in nucleic acid sequences. BMC Genomics. 2014 Oct 23;15:925. DOI: 10.1186/1471-2164-15-925ca
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-15-925
dc.identifier.issn 1471-2164ca
dc.identifier.uri http://hdl.handle.net/10230/25424
dc.language.iso engca
dc.publisher BioMed Centralca
dc.relation.ispartof BMC Genomics. 2014 Oct 23;15:925
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/SAF2011-26211
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/SEV-2012-0208
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/4.0
dc.subject.other Àcids nucleics
dc.title SeAMotE: a method for high-throughput motif discovery in nucleic acid sequencesca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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