UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
Name
Newburger-2009-UniPROBE.pdf
Size
4.09 MB
Format
Adobe PDF
Checksum (MD5)
f4bc255d5e005c7967ef1807774d508d
Author(s)
Bulyk, Martha L.
Newburger, Daniel E.
Date Issued
October 2008
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Citation
Newburger, D. E., and M. L. Bulyk. “UniPROBE: An Online Database of Protein Binding Microarray Data on protein-DNA Interactions.” Nucleic Acids Research 37.Database (2009): D77–D82.
Version
Final published version
Abstract
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/.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gkn660
