NCBI retires Clone DB


Earlier this year, NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post. Links to Clone DB from the NCBI home page will also be going away.

At this time, Clone DB content will be frozen. This static collection of clones will continue to be aligned to newly annotated RefSeq assemblies to generate clone placements, and the Clone FTP site will remain available. The FTP site hosts files that provide access to the sequence, genome placement, and metadata for genomic clones and libraries that were in Clone DB and previously available from the web pages. A new README file has been added to the FTP site that answers FAQs about clone records, genomic placements, and data access. Furthermore, this YouTube tutorial provides details of file content and use of the Clone FTP site. Topics covered in the FAQ and tutorial address tasks such as:

  1. Finding all libraries for an organism
  2. Finding all clones in a library
  3. Finding a clone with specific sequence (e.g. gene) content
  4. Finding/use clone placements on a specific genome assembly
  5. Finding insert/end sequences for a given clone

Additionally, the placements of clones mapped to RefSeq annotated assemblies are available as tracks in Genome Data Viewer (GDV), NCBI’s genome browser. A pair of companion YouTube tutorials and demos provide an overview of GDV and explanation of the use of clone placements for genome interpretation.

We invite you to also view helpful information related to these changes to Clone DB at the NCBI Support Center.

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