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BMC Genomics. 2014 Oct 23;15:925. doi: 10.1186/1471-2164-15-925.

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

Author information

1
Gene Function and Evolution, Centre for Genomic Regulation (CRG), C/ Dr, Aiguader 88, 08003 Barcelona, Spain. gian.tartaglia@crg.es.

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:

SeAMotE 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.

PMID:
25341390
PMCID:
PMC4223730
DOI:
10.1186/1471-2164-15-925
[Indexed for MEDLINE]
Free PMC Article

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