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NAR Molecular Biology Database Collection entry number 1209
Hume, Maxwell; Barrera, Luis; Gisselbrecht, Steve; Bulyk, Martha

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).


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.

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