UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions
Name
Hume-2014-UniPROBE, update 201.pdf
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1.26 MB
Format
Adobe PDF
Checksum (MD5)
a8c59875cab2647c9c27fd321bd5a24d
Author(s)
Barrera, Luis Alberto
Bulyk, Martha L.
Hume, Maxwell A.
Gisselbrecht, Stephen S.
Date Issued
November 2014
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Hume, Maxwell A., Luis A. Barrera, Stephen S. Gisselbrecht, and Martha L. Bulyk. “UniPROBE, Update 2015: New Tools and Content for the Online Database of Protein-Binding Microarray Data on Protein-DNA Interactions.” Nucleic Acids Research (November 5, 2014).
Version
Final published version
Abstract
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.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1093/nar/gku1045
