Welcome to UniPROBE
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 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 currently hosts DNA binding data for 177 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. The database's web tools (on the right) 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. Please click on each tool's "help" link for more information.
News and Updates
- 10/11/08
- A bug in the Search for TF Binding Sites tool has been corrected. Previously, the tool was incorrectly generating the reverse complement of the user entered sequence, which prevented it from finding reverse complement matches. Although the problem did not give rise to any false positive matches, many true positives may have been missed. We apologize for the inconvenience.
- 09/14/08
- The Downloads section now contains zip files holding data for every protein in the database (whereas before the files were segregated by publication), and it also now contains a zip file holding documentation and SQL code for generating many of the database's tables.
- 08/16/08
- The PBM Database has been updated, renamed, and relocated! This current version of the database is now called the UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) Database, and the "Search for Similar Motifs" and "Search for TF Binding Sites" tools are fully implemented.
- 05/16/08
- The PBM database is now public for the mouse homeodomains data! We recommend that you use either Firefox or Internet Explorer for browsing this site. Questions, comments, and suggestions are most welcome at the database help address (
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If you wish to receive PBM Database updates, which will include the addition of new datasets and data analyses, you are encouraged to register for the website here.