SMART 4.0: towards genomic data integration - PubMed (original) (raw)

SMART 4.0: towards genomic data integration

Ivica Letunic et al. Nucleic Acids Res. 2004.

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.

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Figures

Figure 1

Figure 1

SMART representation of human enteropeptidase precursor (ENSP00000284885). Intron positions are represented by vertical lines, showing intron phase and exact position in AA. Intron positions are taken from Ensembl gene predictions.

Figure 2

Figure 2

SMART representation of an orthologous group alignment. User-supplied proteins are aligned using ClustalW. Domains, intrinsic features and introns are mapped onto the alignment with their positions adjusted according to gaps (black boxes). This tool allows easy visual comparison of intron positions and their relations to protein features.

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