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Nucleic Acids Research Advance Access originally published online on October 8, 2008
Nucleic Acids Research 2009 37(Database issue):D77-D82; doi:10.1093/nar/gkn660
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Nucleic Acids Research, 2009, Vol. 37, Database issue D77-D82
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

UniPROBE: an online database of protein binding microarray data on protein–DNA interactions

Daniel E. Newburger1 and Martha L. Bulyk1,2,3,*

1Division of Genetics, Department of Medicine, 2Department of Pathology, Brigham and Women's Hospital and Harvard Medical School and 3Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 617 525 4725; Fax: +1 617 525 4705; Email: mlbulyk{at}receptor.med.harvard.edu

Received August 15, 2008. Revised September 18, 2008. Accepted September 21, 2008.

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive PBM data on the preferences of proteins for all possible sequence variants (‘words’) of length k (‘k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse and human. Current web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. The UniPROBE database is available at http://thebrain.bwh.harvard.edu/uniprobe/.


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