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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions</title><author><name sortKey="Hume, Maxwell A" sort="Hume, Maxwell A" uniqKey="Hume M" first="Maxwell A." last="Hume">Maxwell A. Hume</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF2">Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Barrera, Luis A" sort="Barrera, Luis A" uniqKey="Barrera L" first="Luis A." last="Barrera">Luis A. Barrera</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Gisselbrecht, Stephen S" sort="Gisselbrecht, Stephen S" uniqKey="Gisselbrecht S" first="Stephen S." last="Gisselbrecht">Stephen S. Gisselbrecht</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF5">Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25378322</idno><idno type="pmc">4383892</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383892</idno><idno type="RBID">PMC:4383892</idno><idno type="doi">10.1093/nar/gku1045</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000F39</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F39</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions</title><author><name sortKey="Hume, Maxwell A" sort="Hume, Maxwell A" uniqKey="Hume M" first="Maxwell A." last="Hume">Maxwell A. Hume</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF2">Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Barrera, Luis A" sort="Barrera, Luis A" uniqKey="Barrera L" first="Luis A." last="Barrera">Luis A. Barrera</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Gisselbrecht, Stephen S" sort="Gisselbrecht, Stephen S" uniqKey="Gisselbrecht S" first="Stephen S." last="Gisselbrecht">Stephen S. Gisselbrecht</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><affiliation><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF3">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF4">Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation><affiliation><nlm:aff id="AFF5">Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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 <italic>in vitro</italic> data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length <italic>k</italic> (‘<italic>k</italic>-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of <italic>k</italic>-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 <ext-link ext-link-type="uri" xlink:href="http://uniprobe.org">http://uniprobe.org</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Berger, M F" uniqKey="Berger M">M.F. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25378322</article-id><article-id pub-id-type="pmc">4383892</article-id><article-id pub-id-type="doi">10.1093/nar/gku1045</article-id><article-categories><subj-group subj-group-type="heading"><subject>Database Issue</subject></subj-group></article-categories><title-group><article-title>UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hume</surname><given-names>Maxwell A.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF2"><sup>2</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-2877-8079</contrib-id></contrib><contrib contrib-type="author"><name><surname>Barrera</surname><given-names>Luis A.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF3"><sup>3</sup></xref><xref ref-type="aff" rid="AFF4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gisselbrecht</surname><given-names>Stephen S.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bulyk</surname><given-names>Martha L.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF3"><sup>3</sup></xref><xref ref-type="aff" rid="AFF4"><sup>4</sup></xref><xref ref-type="aff" rid="AFF5"><sup>5</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><aff id="AFF1"><label>1</label>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</aff><aff id="AFF2"><label>2</label>Bioinformatics Graduate Program, Northeastern University, Boston, MA 02115, USA</aff><aff id="AFF3"><label>3</label>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA</aff><aff id="AFF4"><label>4</label>Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA</aff><aff id="AFF5"><label>5</label>Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>To whom correspondence should be addressed. Tel: +1 617 525 4725; Fax: +1 617 525 4705; Email: <email>mlbulyk@receptor.med.harvard.edu</email></corresp></author-notes><pub-date pub-type="ppub"><day>28</day><month>1</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>05</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>05</day><month>11</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>43</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D117</fpage><lpage>D122</lpage><history><date date-type="accepted"><day>12</day><month>10</month><year>2014</year></date><date date-type="received"><day>15</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact <email>journals.permissions@oup.com</email></license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="gku1045.pdf"></self-uri><abstract><p>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 <italic>in vitro</italic> data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length <italic>k</italic> (‘<italic>k</italic>-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of <italic>k</italic>-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 <ext-link ext-link-type="uri" xlink:href="http://uniprobe.org">http://uniprobe.org</ext-link>.</p></abstract><counts><page-count count="6"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>28 January 2015</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec sec-type="intro" id="SEC1"><title>INTRODUCTION</title><p>Characterizing and predicting transcription factor (TF) DNA-binding specificities are crucial tasks for understanding the functioning of cellular regulatory networks. The particular binding affinities of a TF govern its set of target genes and thus play an important role in cellular functions and differentiation. The development of universal protein-binding microarray (PBM) technology (<xref rid="B1" ref-type="bibr">1</xref>) has allowed for comprehensive high-resolution profiling of the DNA-binding specificity of a given TF by evaluating its binding affinity for all possible <italic>k</italic>-mer DNA sequences. The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) database (<xref rid="B2" ref-type="bibr">2</xref>) was created to provide appropriate curation, easy searching and an informative display interface for universal PBM data.</p><p>An update to UniPROBE was published in 2011 (<xref rid="B3" ref-type="bibr">3</xref>). Since that time, many new features have been added to the web interface. In addition, numerous data sets have been deposited into UniPROBE. Here, we discuss these data and features, which include a new data deposition pipeline, a negative control sequence generation tool and motifs derived using BEEML-PBM (<xref rid="B4" ref-type="bibr">4</xref>).</p></sec><sec id="SEC2"><title>DATABASE ADDITIONS</title><p>Table <xref ref-type="table" rid="tbl1">1</xref> describes 12 new publications whose PBM data sets have been introduced into UniPROBE since the last update (<xref rid="B5" ref-type="bibr">5</xref>–<xref rid="B16" ref-type="bibr">16</xref>). The 96 TFs from these publications come from 19 highly diverse species, many of which are new to the database. At the time of this manuscript's preparation, UniPROBE hosts 515 non-redundant proteins and complexes. A number of additional data depositions are planned for the near future: e.g. Nowak-Lovato <italic>et al.</italic>, 2012 (<xref rid="B17" ref-type="bibr">17</xref>); Weirauch <italic>et al.</italic>, 2013 (<xref rid="B18" ref-type="bibr">18</xref>); Siggers <italic>et al.</italic>, 2014 (<xref rid="B19" ref-type="bibr">19</xref>); Lindemose <italic>et al.</italic>, 2014 (<xref rid="B20" ref-type="bibr">20</xref>); Oberstaller <italic>et al.</italic>, 2014 (<xref rid="B21" ref-type="bibr">21</xref>). We anticipate that most future depositions will likely be performed by the authors themselves using our new data deposition pipeline.</p><table-wrap id="tbl1" position="float"><label>Table 1.</label><caption><title>New PBM data sets added into UniPROBE</title></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Reference</th><th align="left" rowspan="1" colspan="1">Number of proteins or complexes</th><th align="left" rowspan="1" colspan="1">Species</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Alibés <italic>et al.</italic> (<xref rid="B5" ref-type="bibr">5</xref>)</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"><italic>Homo sapiens</italic>, <italic>Saccharomyces cerevisiae</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Campbell <italic>et al.</italic> (<xref rid="B6" ref-type="bibr">6</xref>)</td><td align="left" rowspan="1" colspan="1">19</td><td align="left" rowspan="1" colspan="1"><italic>Plasmodium falciparum</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Gordân <italic>et al.</italic> (<xref rid="B7" ref-type="bibr">7</xref>)</td><td align="left" rowspan="1" colspan="1">27</td><td align="left" rowspan="1" colspan="1"><italic>S. cerevisiae</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Del Bianco <italic>et al.</italic> (<xref rid="B8" ref-type="bibr">8</xref>)</td><td align="left" rowspan="1" colspan="1">9</td><td align="left" rowspan="1" colspan="1"><italic>H. sapiens</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Cheatle Jarvela <italic>et al.</italic> (<xref rid="B9" ref-type="bibr">9</xref>)</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1"><italic>Patiria miniata</italic>, <italic>Strongylocentrotus purpuratus</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Busser <italic>et al.</italic> (<italic>Development</italic>) (<xref rid="B10" ref-type="bibr">10</xref>)</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1"><italic>Drosophila melanogaster</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Nakagawa <italic>et al.</italic> (<xref rid="B11" ref-type="bibr">11</xref>)</td><td align="left" rowspan="1" colspan="1">20</td><td align="left" rowspan="1" colspan="1"><italic>Acanthamoeba castellanii</italic>, <italic>Allomyces macrogynus</italic>, <italic>Ashbya gossypii</italic>, <italic>Aspergillus nidulans</italic>, <italic>D. melanogaster</italic>, <italic>H. sapiens</italic>, <italic>Kluyveromyces lactis</italic>, <italic>Monosiga brevicollis</italic>, <italic>Mus musculus</italic>, <italic>Mycosphaerella graminicola</italic>, <italic>Nematostella vectensis</italic>, <italic>S. purpuratus</italic>, <italic>Trichoplax adhaerens</italic>, <italic>Tuber melanosporum</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Soruco <italic>et al.</italic> (<xref rid="B12" ref-type="bibr">12</xref>)</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"><italic>D. melanogaster</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Busser <italic>et al.</italic> (<italic>PNAS</italic>) (<xref rid="B13" ref-type="bibr">13</xref>)</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"><italic>D. melanogaster</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Peterson <italic>et al.</italic> (<xref rid="B14" ref-type="bibr">14</xref>)</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1"><italic>M. musculus</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">De Masi <italic>et al.</italic> (<xref rid="B15" ref-type="bibr">15</xref>)</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"><italic>Caenorhabditis elegans</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Helfer <italic>et al.</italic> (<xref rid="B16" ref-type="bibr">16</xref>)</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">Total number of new proteins/complexes:</td><td colspan="2" align="center" rowspan="1">96</td></tr><tr><td align="left" rowspan="1" colspan="1">Total, last described (<xref rid="B3" ref-type="bibr">3</xref>):</td><td colspan="2" align="center" rowspan="1">404</td></tr><tr><td align="left" rowspan="1" colspan="1">Total number of non-redundant proteins/complexes in UniPROBE:</td><td colspan="2" align="center" rowspan="1">515</td></tr></tbody></table></table-wrap></sec><sec id="SEC3"><title>DATA DEPOSITION PIPELINE</title><p>Among the most significant features recently added to UniPROBE is a web-based pipeline for deposition of new PBM data sets. The link for this tool is found conveniently in a header near the top of the front page or by accessing it directly by URL at <ext-link ext-link-type="uri" xlink:href="http://thebrain.bwh.harvard.edu/pbms/webworks_pub_dev/admin.php">http://thebrain.bwh.harvard.edu/pbms/webworks_pub_dev/admin.php</ext-link>. Previously, uploading data manually into the MySQL database was inefficient and error-prone; therefore, we designed several linked scripts to automate the process.</p><p>Figure <xref ref-type="fig" rid="F1">1A</xref> shows the main page for this pipeline, which also outlines the control flow of the deposition for users. In the first five steps, the user can input information into the database concerning the proteins involved in their study. While the most convenient way to do this is by preparing an appropriately formatted spreadsheet file (for steps 2, 4 and 5; see Figure <xref ref-type="fig" rid="F1">1B</xref>), alternatively the input can be done one entry at a time using an HTML form if a user prefers that method. Currently, the user must prepare a folder with all of the data files they wish to make public. Instructions for data file preparation are given (and are also provided in Supplementary Text 1), and several helpful scripts are available for download to aid the process. The user then uploads the folder to the UniPROBE server as a zip file. The remaining steps fully integrate the data files into the web interface, including constructing sequence logos for each protein and making all the data easily searchable and available for download. The UniPROBE administrator will then finalize the deposition by ensuring proper insertion and moving the new data into the public version of the web site. Data depositors may contact the UniPROBE administrator to specify a release date for prepublication data submissions.</p><fig id="F1" position="float"><label>Figure 1.</label><caption><p>Data deposition pipeline. (<bold>A</bold>) The main page for the UniPROBE data deposition pipeline provides an outline of the data deposition procedure. The user successively clicks each link and follows the instructions in each step. Some steps require only the click of a button, whereas others require either submission of an input file or some extra actions on the command line. (<bold>B</bold>) The instructions for file-based input in step 5. Steps 2 and 4 have similar instructions. File-based input makes it easy for the user to simultaneously provide all the relevant information to add to the database, and has formatting, error checking and rollback functionality built in.</p></caption><graphic xlink:href="gku1045fig1"></graphic></fig></sec><sec id="SEC4"><title>INCORPORATION OF BEEML-PBM MOTIFS</title><p>All of the raw PBM data posted in UniPROBE until recently have been handled in the same manner: the Seed-and-Wobble algorithm, introduced jointly with universal PBM technology (<xref rid="B1" ref-type="bibr">1</xref>,<xref rid="B22" ref-type="bibr">22</xref>), is used to generate a position weight matrix (PWM) (<xref rid="B23" ref-type="bibr">23</xref>,<xref rid="B24" ref-type="bibr">24</xref>), which in turn is used to generate sequence logos (<xref rid="B25" ref-type="bibr">25</xref>) that are displayed on the protein's Details page (e.g. see Figure <xref ref-type="fig" rid="F2">2A</xref>). Since the development of universal PBM technology, other algorithms have been developed to derive PWMs from the PBM data. BEEML-PBM employs a maximum likelihood approach, using a weighted nonlinear least-squares regression to infer free energy parameters for TF–DNA interactions (<xref rid="B4" ref-type="bibr">4</xref>). BEEML-PBM was one of the top two algorithms in the DREAM5 challenge (<xref rid="B18" ref-type="bibr">18</xref>) and provided PWMs with better performance than Seed-and-Wobble for the majority of TFs. We have generated PWMs using BEEML-PBM for the PBM data from all publications whose data have been incorporated into UniPROBE, including those mentioned in this paper (<xref rid="B1" ref-type="bibr">1</xref>,<xref rid="B5" ref-type="bibr">5</xref>–<xref rid="B16" ref-type="bibr">16</xref>,<xref rid="B26" ref-type="bibr">26</xref>–<xref rid="B32" ref-type="bibr">32</xref>). The free energy parameters derived from BEEML-PBM were converted into PWM frequencies by applying a Boltzmann distribution probability mass function to each matrix column. Figure <xref ref-type="fig" rid="F2">2</xref> shows an example of Seed-and-Wobble and BEEML-PBM logos in UniPROBE. All of the new logos are currently viewable on the appropriate protein pages and the PWMs are available for download either individually on these pages or in bulk on the Downloads page.</p><fig id="F2" position="float"><label>Figure 2.</label><caption><p>Seed-and-Wobble and BEEML-PBM motif displays. Examples of displays for data generated using the (A) Seed-and-Wobble and (B) BEEML-PBM algorithms for the Erg protein, from Wei <italic>et al.</italic>, 2010 (<xref rid="B31" ref-type="bibr">31</xref>). (<bold>A</bold>) The Seed-and-Wobble data displays a sequence logo, links for downloading the PWM data and the top-scoring k-mer along with its PBM enrichment score. (<bold>B</bold>) The BEEML-PBM data display format is essentially the same, but because k-mers and enrichment scores are not utilized in this algorithm, an IUPAC consensus sequence derived from the PWM is instead displayed above the motif. The reverse complement sequence orientation can be displayed for either data set individually by clicking the appropriate button; this changes the logo, the PWM file link and the displayed sequence. Assignment of ‘forward’ versus ‘reverse complement’ orientation is arbitrary for each PWM—here, the BEEML-PBM data have been switched to ‘reverse complement’ mode in order to display a more obvious comparison between the logos, since its ‘forward’ orientation happens to correspond more closely to the Seed-and-Wobble data's ‘reverse complement’ orientation.</p></caption><graphic xlink:href="gku1045fig2"></graphic></fig></sec><sec id="SEC5"><title>NEGATIVE CONTROL SEQUENCE GENERATOR</title><p>UniPROBE's main ‘toolbox’, found on the front and Browse pages, includes: a basic text search with different options; a tool that finds proteins with a sufficiently close match to a query DNA motif; a tool that scans a DNA sequence for putative TF-binding sites (<xref rid="B2" ref-type="bibr">2</xref>); and a blastp search tool for matching protein sequences (<xref rid="B3" ref-type="bibr">3</xref>). In addition to predicting specific protein–DNA interactions, it is sometimes desirable to find a sequence that is predicted not to be bound by a given protein(s); e.g. when designing negative controls for <italic>in vivo</italic> reporter experiments or nonspecific competitor DNA for <italic>in vitro</italic> assays. An important new addition to this toolbox is a negative control (nonbinding) sequence generator for such purposes; the search interface for this tool is displayed in Figure <xref ref-type="fig" rid="F3">3A</xref>. This tool takes a list of proteins stored in UniPROBE as input along with a few parameters (PBM <italic>k</italic>-mer enrichment score threshold for TF binding and minimum and maximum length cutoffs) for the desired sequence to be generated. The output is a DNA sequence which is predicted to have little to no specific binding by any of the proteins selected as input based on the PBM data available for that protein in UniPROBE.</p><fig id="F3" position="float"><label>Figure 3.</label><caption><p>Examples of input and output from the Negative Control Sequence Generator tool. (<bold>A</bold>) Form for the Negative Control Sequence Generator tool. In this example, the user has selected two proteins using the pulldown menu, but alternatively, the user can select all proteins in the database from a given species or enter the proteins he/she wants into the text area. The user has requested two sequences between 50 and 150 bp in length. The enrichment score threshold and ‘maximum number of tries’ parameter values used here are the defaults. Clicking on the ‘Help’ link in this box on the web page provides more information about the various parameters. (<bold>B</bold>) The text of an email reply containing the results from the Negative Control Sequence Generator tool for the input shown in (A).</p></caption><graphic xlink:href="gku1045fig3"></graphic></fig><p>Briefly, the algorithm works as follows. First, it assembles a list of all contiguous 8-mers such that every selected protein has scored below the enrichment score threshold for binding to that 8-mer in every PBM data set for that protein. Then, it generates putative nonbinding DNA sequences by randomly concatenating suitable <italic>k</italic>-mers such that no disallowed 8-mer—i.e. no 8-mer not in the input list—will appear at any point in the sequence. This is ensured by the construction and use of a mapping in which every 7-mer corresponds to a list of the bases allowed to directly follow it in the next sequential nucleotide. During each addition to the sequence, the next nucleotide added is selected from this list to ensure that no disallowed 8-mer is created. Note that since the addition of <italic>k</italic>-mers is performed randomly, this algorithm is non-deterministic; thus, the user can also specify the number of sequences to be generated. The results are emailed to the user once the computation has finished; an example is provided in Figure <xref ref-type="fig" rid="F3">3B</xref>.</p></sec><sec id="SEC6"><title>OTHER NEW FEATURES</title><p>The blastp search feature introduced in the last published update (<xref rid="B3" ref-type="bibr">3</xref>) has been further improved by adding a visualization of the alignment between the query and result sequences within the search results.</p><p>Links to the TFBSshape database (<xref rid="B33" ref-type="bibr">33</xref>) have been included in the Details pages of proteins with available TFBSshape data. TFBSshape describes the structural features of DNA at TF binding sites, and has entries for proteins corresponding to entries in JASPAR (<xref rid="B34" ref-type="bibr">34</xref>,<xref rid="B35" ref-type="bibr">35</xref>) and UniPROBE. Figure <xref ref-type="fig" rid="F4">4</xref> shows an example of a link and its corresponding TFBSshape web page. Publications with data in UniPROBE whose protein pages currently link to TFBSshape (and vice versa) are: Berger <italic>et al.</italic>, 2006 (<xref rid="B1" ref-type="bibr">1</xref>); Berger <italic>et al.</italic>, 2008 (<xref rid="B26" ref-type="bibr">26</xref>); Zhu <italic>et al.</italic>, 2009 (<xref rid="B27" ref-type="bibr">27</xref>); Badis <italic>et al.</italic>, 2009 (<xref rid="B28" ref-type="bibr">28</xref>); Lesch <italic>et al.</italic>, 2009 (<xref rid="B30" ref-type="bibr">30</xref>); Scharer <italic>et al.</italic>, 2009 (<xref rid="B32" ref-type="bibr">32</xref>). We will continue to correspond with the TFBSshape administrators and provide links for additional publications as they become available in the TFBSshape database.</p><fig id="F4" position="float"><label>Figure 4.</label><caption><p>TFBSshape links. (<bold>A</bold>) An example of a link to the TFBSshape database from the Protein Details page for Hoxa6, from Berger <italic>et al.</italic>, 2008 (<xref rid="B26" ref-type="bibr">26</xref>). (<bold>B</bold>) The TFBSshape page for Hoxa6, to which the link in (A) leads.</p></caption><graphic xlink:href="gku1045fig4"></graphic></fig><p>Finally, migration to a new, faster server has been completed, and we expect a concomitant speedup in web operation times.</p></sec><sec sec-type="discussion" id="SEC7"><title>DISCUSSION</title><p>There are many opportunities for further improvements to UniPROBE in the near future. To start, there are additional published PBM data sets still awaiting deposition into the database. To expedite data deposition, we encourage authors of such studies to submit their data themselves into UniPROBE using our new data deposition pipeline.</p><p>Additional improvements could be made to the data deposition pipeline. Currently, the pipeline does not account explicitly for variations in the structure of the data files available for download from each publication; for example each protein from a publication may have different sets of PBM data reflecting distinct binding activity for different clones, protein complexes of which a particular protein is a component or data from replicate PBM experiments. In some cases, data are available from experiments using different PBM array versions (which may themselves have multiple replicates).</p><p>Similarly, the structure of the Protein Details page must properly match the file structure in order to optimally display the data. The default template for the Details page has not yet been configured to handle the amount of potential variability in the file structure, and currently a new template page must be generated by the database administrator for any publication newly deposited into UniPROBE that does not have strictly one set of files per protein, without any complexes. In the future, we hope to automate this process by creating one or more pre-written page templates that can handle variation in data file structure. Users should still be able to request customization of their publication's Details pages if necessary.</p><p>Further planned improvements to the deposition process include the ability to request specific UniPROBE accession numbers for proteins (see Robasky and Bulyk, 2011 (<xref rid="B3" ref-type="bibr">3</xref>) for a description of protein accession numbers in UniPROBE). We also plan to generate accession numbers to publications for reference and to allow users to specify particular publication data sets for searches.</p><p>PWM data derived using other motif finding algorithms in addition to Seed-and-Wobble and BEEML-PBM will also be added. Among those on which we may choose to focus initially are FeatureREDUCE (manuscript in preparation) and MatrixREDUCE (<xref rid="B36" ref-type="bibr">36</xref>), which also performed well in the DREAM5 challenge (<xref rid="B18" ref-type="bibr">18</xref>). BEEML-PBM data will also be generated for the remaining publications that have been deposited in UniPROBE.</p><p>Finally, users will also soon be able to do a bulk download as a FASTA file of the protein sequences of all the TF clones used in the PBM experiments.</p><p>We welcome feedback and suggestions for further improvements from our users. A new UniPROBE administrative email account can now be reached with any questions, comments or suggestions at <email>uniprobe@genetics.med.harvard.edu</email>.</p></sec><sec id="SEC8"><title>AVAILABILITY</title><p>As before, the data in UniPROBE are freely available at the database web site (<ext-link ext-link-type="uri" xlink:href="http://uniprobe.org">http://uniprobe.org</ext-link>), and the sequences of the 60-mer DNA probes on the custom-designed oligonucleotide arrays are available under the terms of an academic research use license available at <ext-link ext-link-type="uri" xlink:href="http://thebrain.bwh.harvard.edu/uniprobe/academic-license.php">http://thebrain.bwh.harvard.edu/uniprobe/academic-license.php</ext-link>.</p></sec><sec sec-type="supplementary-material" id="SEC9"><title>SUPPLEMENTARY DATA</title><p><ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/lookup/suppl/doi:10.1093/nar/gku1045/-/DC1">Supplementary Data</ext-link> are available at NAR Online.</p></sec></body><back><ack><p>We thank Ivan Adzhubey for technical assistance, Chirag Parmar for work on documentation and Kimberly Robasky for helpful discussions.</p></ack><sec id="SEC10"><title>FUNDING</title><p>National Institutes of Health [R01 HG003985 to M.L.B.]; National Science Foundation Graduate Research Fellowship [to L.A.B.]. 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