Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
نویسندگان
چکیده
منابع مشابه
SCOPE: a web server for practical de novo motif discovery
SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on exper...
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A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been propose...
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A complete understanding of transcriptional regulatory processes in the cell requires identification of transcription factor binding sites on a genomewide scale. Unfortunately, these binding sites are typically short and degenerate, posing a significant statistical challenge: many more matches to known transcription factor binding sites occur in the genome than are actually functional. Chromati...
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Summary: High-throughput sequencing technologies such as ChIPseq have deepened our understanding in many biological processes. De novo motif search is one of the key downstream computational analysis following the ChIP-seq experiments and several algorithms have been proposed for this purpose. However, most webbased systems do not perform independent filtering or enrichment analyses to ensure t...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2019
ISSN: 1471-2105
DOI: 10.1186/s12859-019-2686-8