title: SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.
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.
authors.forename: Federico
authors.initials: F
authors.lastname: Agostini
authors.forename: Davide
authors.initials: D
authors.lastname: Cirillo
authors.forename: Riccardo Delli
authors.initials: RD
authors.lastname: Ponti
authors.affiliation: Gene Function and Evolution, Centre for Genomic Regulation (CRG), C/ Dr, Aiguader 88, 08003 Barcelona, Spain. gian.tartaglia@crg.es.
authors.forename: Gian Gaetano
authors.initials: GG
authors.lastname: Tartaglia
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA