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UniPROBE – The Universal PBM Resource for Oligonucleotide Binding Evaluation

NAR Molecular Biology Database Collection entry number 1209
Hume, Maxwell A. (1,2); Barrera, Luis A. (1,3,4); Gisselbrecht, Stephen S. (1); Bulyk, Martha L. (1,3,4,5)
1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115 2 Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115 3 Commitee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138 4 Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115 5 Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115

Database Description

UniPROBE hosts published data generated using universal protein binding microarray (PBM) technology (1), which characterizes transcription factor binding specificity for all possible DNA sequences of a given length, usually 8 to 10 bp. The data for each protein from each publication included in the database receives its own detailed web page, which displays information about the motifs found in the form of sequence logos, as well as an informative summary of the protein and the clone sequences used. The data files used to generate the displays are all publicly available for download either individually from the display page or in bulk from the downloads page. A copy of the database's content as SQL is also publicly available for those who want to install a local copy on their computer. The site also has a “toolbox” comprising the following web-based tools: a search tool to query the database quickly using one or more fields; a motif-searching tool, which will scan the database for a motif similar to one that is supplied as input in one of several possible formats; a transcription factor binding site (TFBS) search tool, which will scan a supplied DNA sequence for possible TFBSs; a blastp search tool that will look for proteins with similar amino acid sequence to one that is supplied as input; and a new negative sequence control generator tool (see below). Researchers who want to deposit universal PBM data into UniPROBE can now use a publicly available deposition tool to accomplish this (see below).

Recent Developments

UniPROBE's web functionality has undergone many significant upgrades. Now available is a publicly available, streamlined data deposition pipeline, which aims to automate and ease the data insertion process for researchers who want to store and display their PBM data. A new negative control sequence generator tool is also available in the web toolbox, which generates a DNA sequence predicted to have no residual binding by any of a set of proteins from the database which are supplied as input, based on the PBM data stored for these proteins and a set of user-specified parameters. BEEML-PBM motifs are now displayed as sequence logos on the protein details pages, with the corresponding position weight matrix (PWM) data also available for download. Links to corresponding pages in the TFBSshape database (2), which provides structural information on DNA sequences corresponding to binding sites for specific transcription factors as dictated by UniPROBE, are provided for all proteins currently in TFBSshape. Lastly, new data from various publications have been added to UniPROBE. All recent updates can be found on the front page of the site.


1. Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W., 3rd and Bulyk, M.L. (2006) Compact, universal DNA microarrays to comprehensively determine trnscription factor binding site specificities. Nat Biotechnol, 24, 1429-1435.
2. Yang, L., Zhou, T., Dror, I., Mathelier, A., Wasserman, W.W., Gordan, R. and Rohs, R. (2014) TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res., 42, D148-D155.

Go to the abstract in the NAR 2009 Database Issue.
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