UniPROBE: an online database of protein binding microarray data on protein–DNA interactions
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...
| Main Authors: | , |
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| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press (OUP)
2012
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| Online Access: | http://hdl.handle.net/1721.1/73095 |
| _version_ | 1826213475101179904 |
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| author | Bulyk, Martha L. Newburger, Daniel E. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Bulyk, Martha L. Newburger, Daniel E. |
| author_sort | Bulyk, Martha L. |
| collection | MIT |
| description | 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/. |
| first_indexed | 2024-09-23T15:49:48Z |
| format | Article |
| id | mit-1721.1/73095 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:49:48Z |
| publishDate | 2012 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | mit-1721.1/730952022-10-02T04:22:35Z UniPROBE: an online database of protein binding microarray data on protein–DNA interactions Bulyk, Martha L. Newburger, Daniel E. Harvard University--MIT Division of Health Sciences and Technology Bulyk, Martha L. 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/. National Institutes of Health (U.S.) (Grant R01 HG003985) 2012-09-21T13:01:39Z 2012-09-21T13:01:39Z 2008-10 2008-09 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/73095 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. en_US http://dx.doi.org/10.1093/nar/gkn660 Nucleic Acids Research Creative Commons Attribution Non-Commercial http://creativecommons.org/licenses/by-nc/2.5 application/pdf Oxford University Press (OUP) Oxford |
| spellingShingle | Bulyk, Martha L. Newburger, Daniel E. UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title | UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title_full | UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title_fullStr | UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title_full_unstemmed | UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title_short | UniPROBE: an online database of protein binding microarray data on protein–DNA interactions |
| title_sort | uniprobe an online database of protein binding microarray data on protein dna interactions |
| url | http://hdl.handle.net/1721.1/73095 |
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