STREME: Accurate and versatile sequence motif discovery.

ABSTRACT: Sequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences-for example, the binding site motifs of DNA-and RNA-binding proteins. The STREME algorithm presented here advances the state-of-the-art in ab initio motif discovery in terms of both accuracy and versatility. Using in vivo DNA (ChIP-seq) and RNA (CLIP-seq) data, and validating motifs with reference motifs derived from in vitro data, we show that STREME is more accurate, sensitive and thorough than several widely used algorithms (DREME, HOMER, MEME, Peak-motifs) and two other representative algorithms (ProSampler and Weeder). STREME's capabilities include the ability to find motifs in datasets with hundreds of thousands of sequences, to find both short

SUBMITTER: Bailey TL 

PROVIDER: S-EPMC8479671 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature