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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Generic eukaryotic core promoter prediction using structural features of DNA
Genome Research, Volume 18, No. 2, Year 2008
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Description
Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists. ©2008 by Cold Spring Harbor Laboratory Press.
Authors & Co-Authors
Abeel, Thomas
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Saeys, Yvan
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Rouzé, Pierre
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Van de Peer, Y.
Belgium, Ghent
Vlaams Instituut Voor Biotechnologie
Belgium, Ghent
Universiteit Gent
Statistics
Citations: 165
Authors: 4
Affiliations: 2
Identifiers
Doi:
10.1101/gr.6991408
ISSN:
15495469
Research Areas
Genetics And Genomics