Connecting the Lab to the Genome: CloneDB

The ever-expanding availability of genome sequences from a variety of organisms has transformed the way researchers can approach biological questions. However, there is still a need to associate genomic sequence with physical reagents that can be used to perform experiments. NCBI has developed a resource to facilitate this association for one important reagent, namely clones. It has historically been difficult for researchers to take full advantage of the wealth of information associated with clone types, as data and metadata have been stored in disparate databases. The NCBI Clone DB provides integrated information for both vector-based and cell-based clones, including sequence data, map positions, gene content and distributor information (http://www.ncbi.nlm.nih.gov/clone/). Data is available for hundreds of genomic and cell-based clones and libraries from a diverse range of animal and plant taxa. Library browsers permit viewing of high-level information, while library-specific pages contain detailed information on library construction and distributors. The database can be searched by clone name, accession, mapping position and features such as genes. Newly developed display pages for individual clones provide an integrated view of the data stored for each clone, and link to relevant NCBI resources. Data from Clone DB is currently displayed in the NCBI MapViewer, which permits the simultaneous viewing of annotation tracks based on different coordinate systems, and in CloneFinder, a tool that permits location-based searches for clones in a graphical interface. We will present examples of clone data and demonstrate the features of the interfaces and associated tools.