NCBI to retire Clone DB web interface

NCBI to retire Clone DB web interface

Starting in April 2019, the sequence content of Clone DB will be frozen, and its web interfaces will no longer be available. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI’s Genome Data Viewer (GDV) using the sequence data currently in Clone DB. These placements and their corresponding underlying (now static) library and sequence data will also be accessible on the Clone DB FTP site.

The collection of Clone DB records for cell-based (integrated) gene targeting and gene trap libraries will also be retired in January. These data were provided to Clone DB by MGI.  Clone DB users should refer to MGI for their continuing research needs.

Please contact us with any comments, concerns, or if you need help with the use of Clone DB data.

Clone DB was originally implemented as the Clone Registry during the human and mouse genome projects. In subsequent years, it expanded to represent clone-associated data for a broad range of organisms. Clone DB has been a valuable resource connecting users with information and reagents for genomic and cell-based clones. However, with the advent of short read sequencing, fewer and fewer genomic clone end and insert sequences are submitted to NCBI every year, and the usage of and need for Clone DB has dropped significantly.

6 thoughts on “NCBI to retire Clone DB web interface

  1. Cloned environmental sequences of soil fungi and endophytes are especially valuable within a blast search and inform users of similar findings. I don’t see these as available on the clone FTP site

  2. This is an actively used resource among many genomics research groups.
    Strange that cloneDB will be taken down. With short read NGS, we select clones
    regularly for targeted purposes, so access to available clones and where they sit in genomes is vital. It is also unclear if it will be possible to visualize clone ends as a cloneDB track on the GDV or not. It seems to work right now. Hoping this will at least still be available. This resource as it seems to me is unnecessary to remove, especially if it was a considerable effort during the genome projects (essentially genome projects will never cease!)

  3. Hello dear colleagues.
    What could you do to map and obtain the sequences of contig 1065 and contig 45 of chromosome 4, from the Drosophila Buzzatti BAC library.
    Thanks and regards.
    Sincerely, Francisco García Franco
    Universidad Autónoma Metropolitana. Mexico City.

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