SMART 4.0: towards genomic data integration

Ivica Letunic

Richard Copley

Steffen Schmidt

Francesca Ciccarelli

EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany, ^{Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK,}^{Bioinformatik, Biozentrum, Am Hubland, University of Wuerzburg, 97074 Wuerzburg, Germany and}^{MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK}

^{To whom correspondence should be addressed. Tel: +49 6221 387 526; Fax: +49 6221 387 517; Email:}ed.grebledieh-lbme@krob

Received 2003 Sep 17; Revised 2003 Oct 6; Accepted 2003 Oct 6.

Abstract

SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. The January 2004 release of SMART contains 685 protein domains. New developments in SMART are centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions of orthology. New visualization tools have been developed to allow analysis of gene intron–exon structure within the context of protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same gene. Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.

Abstract

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