ProViz—a web-based visualization tool to investigate the functional and evolutionary features of protein sequences
By Peter Jehl, Jean Manguy, D. Shields, Desmond G. Higgins, Norman E. Davey. 2016
68 citations recorded by the source corpus.
Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/.
Subfields: Molecular Biology
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In Molecular Biology
- Zsuzsanna Dosztányi
- Gábor Erdös
- Bálint Mészáros
- Vladimir N Uversky
- Silvio C. E. Tosatto
- Michele Vendruscolo
- Carlos H. M. Rodrigues
- Arne Elofsson
Citations in the corpus
- A structural biology community assessment of AlphaFold2 applications (2021, methodology): “To facilitate the study of human IDRs, we provide these predictions for human proteins in Supplementary Dataset 1 and in ProViz 23 : http://slim.icr.ac.uk/ projects/alphafold?page=alphafold_proviz_homepage.”
- IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation (2021, background): “Tools, such as Jalview (45) or ProViz (46) can visualize sequence alignment and also show disorder information for a single protein, but they cannot provide information on the evolutionary conservation of IDPs.”
- MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins (2017, methodology): “MobiDB is widely used by scientific community and by third party services such as DisProt (17) and ProViz (61).”