The Limits of De Novo DNA Motif Discovery
نویسندگان
چکیده
منابع مشابه
The Limits of De Novo DNA Motif Discovery
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...
متن کاملSCOPE: 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 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...
متن کاملMotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences
Motivation In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chrom...
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The planted (l, d) motif search is one of the most widely studied problems in bioinformatics, which plays an important role in the identification of transcription factor binding sites in DNA sequences. However, it is still a challenging task to identify highly degenerate motifs, since current algorithms either output the exact results with a high computational cost or accomplish the computation...
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ژورنال
عنوان ژورنال: PLoS ONE
سال: 2012
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0047836