Unknown

Dataset Information

0

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.

SUBMITTER: Agostini F 

PROVIDER: S-EPMC4223730 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

altmetric image

Publications

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

Agostini Federico F   Cirillo Davide D   Ponti Riccardo Delli RD   Tartaglia Gian Gaetano GG  

BMC genomics 20141023


<h4>Background</h4>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.<h4>Results</h4>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  ...[more]

Similar Datasets

| S-EPMC5996464 | biostudies-literature
| S-EPMC3834837 | biostudies-other
| S-EPMC7911868 | biostudies-literature
| S-EPMC6353932 | biostudies-literature
| S-EPMC4245949 | biostudies-literature
| S-EPMC4737176 | biostudies-other
| S-EPMC9067507 | biostudies-literature
| S-EPMC9197077 | biostudies-literature
| S-EPMC7735737 | biostudies-literature
| S-EPMC6339573 | biostudies-literature