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PhosPhAt : the Arabidopsis thaliana phosphorylation site database : an update
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Durek, P., Schmidt, R., Heazlewood, J. L., Jones, Alexandra M., MacLean, Daniel, Nagel, Alexander, Kersten, Birgit and Schulze, W. X. (2010) PhosPhAt : the Arabidopsis thaliana phosphorylation site database : an update. Nucleic Acids Research, Volume 38 (Supplement 1). D828-D834. doi:10.1093/nar/gkp810 ISSN 0305-1048.
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Official URL: http://dx.doi.org/10.1093/nar/gkp810
Abstract
The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows ‘on-the-fly’ prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.
| Item Type: | Journal Article | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QK Botany | ||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
| Library of Congress Subject Headings (LCSH): | Arabidopsis thaliana -- Data processing, Plants -- Phosphorylation | ||||
| Journal or Publication Title: | Nucleic Acids Research | ||||
| Publisher: | Oxford University Press | ||||
| ISSN: | 0305-1048 | ||||
| Official Date: | January 2010 | ||||
| Dates: |
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| Volume: | Volume 38 | ||||
| Number: | Supplement 1 | ||||
| Page Range: | D828-D834 | ||||
| DOI: | 10.1093/nar/gkp810 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||
| Date of first compliant deposit: | 27 December 2015 | ||||
| Date of first compliant Open Access: | 27 December 2015 | ||||
| Funder: | Germany. Bundesministerium für Bildung und Forschung (BMBF), Max-Planck-Gesellschaft zur Förderung der Wissenschaften [Max Planck Society for the Advancement of Science] | ||||
| Grant number: | 0315046 (BMBF), 0315049A (BMBF) |
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