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. 2012 Jan;40(Database issue):D302-5.
doi: 10.1093/nar/gkr931. Epub 2011 Nov 3.

SMART 7: Recent Updates to the Protein Domain Annotation Resource

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Free PMC article

SMART 7: Recent Updates to the Protein Domain Annotation Resource

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

Abstract

SMART (Simple Modular Architecture Research Tool) is an online resource (http://smart.embl.de/) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version. The current release introduces several novel features and a streamlined user interface resulting in a faster and more comfortable workflow. The underlying protein databases were greatly expanded, resulting in a 2-fold increase in number of annotated domains and features. The database of completely sequenced genomes now includes 1133 species, compared to 630 in the previous release. Domain architecture analysis results can now be exported and visualized through the iTOL phylogenetic tree viewer. 'metaSMART' was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets. An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information.

Figures

Figure 1.
Figure 1.
Displaying SMART protein domain architectures in iTOL. New data export features allow users to simply display domain architecture query results on a NCBI taxonomy based phylogenetic tree. Phylogenetic trees are generated on-the-fly by pruning the NCBI taxonomy database (12) and visualized in interactive Tree Of Life (10). (a) SMART was queried for all proteins containing both CUB and CCP domains. (b) Query results visualized on a phylogenetic tree in iTOL.
Figure 2.
Figure 2.
metaSMART, a novel sub resource dedicated to the exploration of domain architectures in metagenomics data sets. (a) metaSMART user interface provides simple access to all available functions. (b) A subset of protein domain architectures present in the Sargasso Sea data set (14). These are not present in other metagenomics data sets or the standard SMART database, and could be pointing to novel functional associations of various domains.

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