Title:
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SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
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Author:
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Agostini, Federico, 1985-; Cirillo, Davide; Delli Ponti, Riccardo; Tartaglia, Gian Gaetano
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Abstract:
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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. |
Abstract:
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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) |
Subject(s):
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-Àcids nucleics |
Rights:
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© 2014 Federico Agostini et al. Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0
http://creativecommons.org/licenses/by/4.0 |
Document type:
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Article Article - Published version |
Published by:
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BioMed Central
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