2020 | Ivica Letunic, Supriya Khedkar and Peer Bork
The article provides an overview of recent updates and new developments in SMART (Simple Modular Architecture Research Tool), a web resource for identifying and annotating protein domains and analyzing protein domain architectures. Key highlights include:
1. **New Domain Models**: SMART version 9 introduces 68 new models for diverse recombinase families and subfamilies, providing a comprehensive overview of mobile element recombinases such as transposase, integrase, relaxase, resolvase, casposase, and Xer-like cellular recombinase.
2. **Updated Protein Databases**: The underlying protein databases have been synchronized with UniProt, Ensembl, and STRING, increasing the total number of annotated domains and protein features available for analysis. The database now contains over 137 million proteins from around 537,000 species, a 2.7-fold increase compared to the previous release.
3. **Optimized Protein Visualization**: The protein visualization engine has been updated to use the latest web technologies, including interactive SVG for protein schematics, which can be zoomed without quality loss and saved as vector graphics. The viewer also allows for interactive selection of protein regions for BLAST analysis.
4. **Expanded Protein Interaction Data**: Protein interaction data has been synchronized with STRING version 11, providing graphical representations of putative interaction partners for over 21 million proteins.
5. **Enhanced Taxonomic Tree Data Export**: The taxonomic tree export has been updated to be compatible with the Interactive Tree of Life (iTOL) version 5, allowing for more detailed visualization and annotation of phylogenetic trees.
6. **Database and Server Optimizations**: The backend database has been optimized to handle the increased number of annotated features, and server hardware has been upgraded to improve processing speed and reduce response times.
These updates enhance the functionality and usability of SMART, making it a valuable tool for researchers in bioinformatics and molecular biology.The article provides an overview of recent updates and new developments in SMART (Simple Modular Architecture Research Tool), a web resource for identifying and annotating protein domains and analyzing protein domain architectures. Key highlights include:
1. **New Domain Models**: SMART version 9 introduces 68 new models for diverse recombinase families and subfamilies, providing a comprehensive overview of mobile element recombinases such as transposase, integrase, relaxase, resolvase, casposase, and Xer-like cellular recombinase.
2. **Updated Protein Databases**: The underlying protein databases have been synchronized with UniProt, Ensembl, and STRING, increasing the total number of annotated domains and protein features available for analysis. The database now contains over 137 million proteins from around 537,000 species, a 2.7-fold increase compared to the previous release.
3. **Optimized Protein Visualization**: The protein visualization engine has been updated to use the latest web technologies, including interactive SVG for protein schematics, which can be zoomed without quality loss and saved as vector graphics. The viewer also allows for interactive selection of protein regions for BLAST analysis.
4. **Expanded Protein Interaction Data**: Protein interaction data has been synchronized with STRING version 11, providing graphical representations of putative interaction partners for over 21 million proteins.
5. **Enhanced Taxonomic Tree Data Export**: The taxonomic tree export has been updated to be compatible with the Interactive Tree of Life (iTOL) version 5, allowing for more detailed visualization and annotation of phylogenetic trees.
6. **Database and Server Optimizations**: The backend database has been optimized to handle the increased number of annotated features, and server hardware has been upgraded to improve processing speed and reduce response times.
These updates enhance the functionality and usability of SMART, making it a valuable tool for researchers in bioinformatics and molecular biology.