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. 2015 Jan;43(Database issue):D257-60.
doi: 10.1093/nar/gku949. Epub 2014 Oct 9.

SMART: Recent Updates, New Developments and Status in 2015

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Free PMC article

SMART: Recent Updates, New Developments and Status in 2015

Ivica Letunic et al. Nucleic Acids Res. .
Free PMC article

Abstract

SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼ 200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's 'Genomic' mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine.

Figures

Figure 1.
Figure 1.
SMART annotation page for protein TEC_HUMAN. (a) Protein schematic representations are displayed using an interactive Flash applet. Schematics are zoomable without quality loss and exportable into high resolution bitmap images. Protein features selected in various data tables are dynamically highlighted directly in the viewer. Using the interactive scale, any protein region can be selected and submitted for further BLAST analysis. (b) The tabbed interface collects various sources of external information about the protein analyzed. (c) A movable and resizable popup dialog displays the most important bits of information for any selected feature, with links to complete annotation.
Figure 2.
Figure 2.
New data sources included in the protein annotation pages and the redesigned taxonomy viewer. (a) A list of post-translational modifications present in the protein, as annotated by PTMcode (11). More than 60 types of modifications are included. (b) Orthologous groups that contain the protein, as annotated by eggNOG (12). Group descriptions and taxonomic classes are listed. (c) New taxonomic breakdown viewer, which supports very large trees and provides quick navigation through the integrated full text search engine.

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