title: SMART 4.0: towards genomic data integration.
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.
authors.affiliation: EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
authors.forename: Ivica
authors.initials: I
authors.lastname: Letunic
authors.forename: Richard R
authors.initials: RR
authors.lastname: Copley
authors.forename: Steffen
authors.initials: S
authors.lastname: Schmidt
authors.forename: Francesca D
authors.initials: FD
authors.lastname: Ciccarelli
authors.forename: Tobias
authors.initials: T
authors.lastname: Doerks
authors.forename: Jörg
authors.initials: J
authors.lastname: Schultz
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D007438:Introns / Q000235:genetics; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020543:Proteome; D040901:Proteomics; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins; D020543:Proteome