UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions

Nucleic Acids Res. 2015 Jan;43(Database issue):D117-22. doi: 10.1093/nar/gku1045. Epub 2014 Nov 5.


The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / metabolism*
  • Databases, Protein*
  • Internet
  • Nucleotide Motifs
  • Protein Array Analysis*
  • Software
  • Transcription Factors / metabolism*


  • DNA-Binding Proteins
  • Transcription Factors
  • DNA