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Bioinformatics Advance Access originally published online on November 30, 2004
Bioinformatics 2005 21(8):1747-1749; doi:10.1093/bioinformatics/bti173
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster

Casey M. Bergman 1,*, Joseph W. Carlson 2,3 and Susan E. Celniker 2,3

1Department of Genetics, University of Cambridge Cambridge CB2 3EH, UK
2Department of Genome Sciences, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA
3Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA

*To whom correspondence should be addressed.

Summary: Despite increasing numbers of computational tools developed to predict cis-regulatory sequences, the availability of high-quality datasets of transcription factor binding sites limits advances in the bioinformatics of gene regulation. Here we present such a dataset based on a systematic literature curation and genome annotation of DNase I footprints for the fruitfly, Drosophila melanogaster. Using the experimental results of 201 primary references, we annotated 1367 binding sites from 87 transcription factors and 101 target genes in the D.melanogaster genome sequence. These data will provide a rich resource for future bioinformatics analyses of transcriptional regulation in Drosophila such as constructing motif models, training cis-regulatory module detectors, benchmarking alignment tools and continued text mining of the extensive literature on transcriptional regulation in this important model organism.

Availability: http://www.flyreg.org/

Contact: cbergman{at}gen.cam.ac.uk


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