ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery
نویسندگان
چکیده
منابع مشابه
STEME: A Robust, Accurate Motif Finder for Large Data Sets
Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME) to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to...
متن کاملDREME: motif discovery in transcription factor ChIP-seq data
MOTIVATION Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF. RESULTS We present DREME, a motif discovery algorithm specifically designed to f...
متن کاملMEME-ChIP: motif analysis of large DNA datasets
MOTIVATION Advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (TF) ChIP-seq experiments. While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets. RESULTS The MEME-ChIP web service is designed t...
متن کاملComments on 'MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets'
The discovery of phosphorylation motifs helps to understand the underlying regulation mechanism and to facilitate the prediction of unknown phosphorylation sites. Several methods have been proposed to detect phosphorylation motifs from phosphoproteomics datasets. A recent article (Wang et al. 2012) published in Bioinformatics developed a new method MMFPh (Maximal Motif Finder for Phosphoproteom...
متن کاملMMFPh: a maximal motif finder for phosphoproteomics datasets
MOTIVATION Protein phosphorylation, driven by specific recognition of substrates by kinases and phosphatases, plays central roles in a variety of important cellular processes such as signaling and enzyme activation. Mass spectrometry enables the determination of phosphorylated peptides (and thereby proteins) in scenarios ranging from targeted in vitro studies to in vivo cell lysates under parti...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2019
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btz290