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CDART finds protein similarities across significant evolutionary distances using sensitive domain profiles rather than direct sequence similarity. Given a protein query sequence, CDART shows the functional domains that make up a protein (as identified by RPS-BLAST) and then lists proteins with a similar domain architecture, as shown in the illustration below. Relying on domain profiles allows CDART to be fast and, because it relies on annotated functional domains, informative.
A query can be submitted as an (a) protein sequence (in the form of a sequence identifier or as sequence data), (b) set of conserved domains (in the form of superfamily cluster IDs, conserved domain accession numbers, or PSSM IDs), or as (c) multiple queries. Alternatively, you can retrieve a protein sequence record from the Entrez Protein database and follow the link for "Related information: Domain Relatives." The help document provides a quick start guide, as well as details about the input required, output display, and the program's features and functions.
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