CD-Search is NCBI's interface to searching the Conserved Domain Database with protein or nucleotide query sequences. It uses RPS-BLAST, a variant of PSI-BLAST, to quickly scan a set of pre-calculated position-specific scoring matrices (PSSMs) with a protein query. The results of CD-Search are presented as an annotation of protein domains on the user query sequence, and can be visualized as domain multiple sequence alignments with embedded user queries. High confidence associations between a query sequence and conserved domains are shown as specific hits. The CD-Search Help provides additional details, including information about running CD-Search locally.