dc.contributor.author |
Agostini, Federico, 1985- |
dc.contributor.author |
Cirillo, Davide |
dc.contributor.author |
Delli Ponti, Riccardo |
dc.contributor.author |
Tartaglia, Gian Gaetano |
dc.date |
2014 |
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: 10.1186/1471-2164-15-925 |
dc.identifier.citation |
1471-2164 |
dc.identifier.citation |
http://dx.doi.org/10.1186/1471-2164-15-925 |
dc.identifier.uri |
http://hdl.handle.net/10230/25424 |
dc.format |
application/pdf |
dc.language.iso |
eng |
dc.publisher |
BioMed Central |
dc.relation |
info:eu-repo/grantAgreement/EC/FP7/309545 |
dc.relation |
info:eu-repo/grantAgreement/ES/3PE/SAF2011-26211 |
dc.relation |
info:eu-repo/grantAgreement/ES/3PE/SEV-2012-0208 |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.rights |
© 2014 Federico Agostini et al. Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0 |
dc.rights |
http://creativecommons.org/licenses/by/4.0 |
dc.subject |
Àcids nucleics |
dc.title |
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences |
dc.type |
info:eu-repo/semantics/article |
dc.type |
info:eu-repo/semantics/publishedVersion |
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.abstract |
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) |