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. 2011 Jan;39(Database issue):D124-8.
doi: 10.1093/nar/gkq992. Epub 2010 Oct 30.

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

Kimberly Robasky  1 , Martha L Bulyk
Affiliations

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

Kimberly Robasky et al. Nucleic Acids Res. 2011 Jan.

Abstract

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide 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 this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

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Figures

Figure 1.
Figure 1.
Blastp search of UniPROBE with human GATA4 protein sequence and default parameter settings for the advanced search options.
Figure 2.
Figure 2.
Results from blastp search of all protein sequences in UniPROBE using the human full-length GATA4 protein sequence as the query.
See this image and copyright information in PMC

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