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Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31.

CD-Search: protein domain annotations on the fly.

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  • 1Computational Biology Branch, NCBI, National Library of Medicine, NIH, Building 38A, Room 5S508, 8600 Rockville Pike, Bethesda, MD 20894, USA.


We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at

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