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Bioinformatics Advance Access originally published online on August 20, 2008
Bioinformatics 2008 24(20):2418-2419; doi:10.1093/bioinformatics/btn443
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation

Jason Persampieri 1, Deborah I. Ritter 1, Daniel Lees 1, Jessica Lehoczky 2, Qiang Li 3, Su Guo 3 and Jeffrey H. Chuang 1,*

1Department of Biology, Boston College, Chestnut Hill, MA 02467, 2Department of Genetics, Harvard Medical School, Boston, MA 02115 and 3Department of Biopharmaceutical Sciences and Center for Human Genetics, University of California, San Francisco, CA 94143, USA

*To whom correspondence should be addressed.


  Abstract

Summary: There are thousands of strongly conserved non-coding elements (CNEs) in vertebrate genomes, and their functions remain largely unknown. However, without biologically relevant criteria for prioritizing them, selecting a particular CNE sequences to study can be haphazard. To address this problem, we present cneViewer—a database and webtool that systematizes information on conserved non-coding DNA elements in zebrafish. A key feature here is the ability to search for CNEs that may be relevant to tissue-specific gene regulation, based on known developmental expression patterns of nearby genes. cneViewer provides this and other organizing features that significantly facilitate experimental design and CNE analysis.

Availability: http://cneviewer.zebrafishcne.org

Contact: chuangj{at}bc.edu

Associate Editor: Dmitrij Frishman

Received on March 19, 2008; revised on August 7, 2008; accepted on August 18, 2008

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