Clone DB Genomic Library Browser FAQs

This page will be periodically updated to include frequently asked questions (FAQs).


1. What is "Clone DB"?

Clone DB has replaced the former NCBI Clone Registry. While the former Clone Registry only contained information about genomic clones and libraries, the new Clone DB will provide integrated clone-centric information for genomic, cDNA and cell-based (gene trap/gene target) libraries and clones. Be on the lookout for new Clone DB pages!

2. How do I register a genomic library with Clone DB?

Please contact Clone DB to register a library.

3. How can I find a specific genomic library in Clone DB?

Filters are provided on the right hand side of the library browser page to help you navigate to a particular library.

4. How can I find a genomic clone that contains a gene or sequence of interest?

Clone DB can be searched using the name or assembly location of a gene of interest. These searches will identify genomic clones that have been placed at the same location as the gene. For detailed searching instructions, please see the Clone DB Help page. Searches of Clone DB will take you to the individual clone records, where you will find detailed information on map position, associated sequences, and other data.

You can also use the NCBI Clone Finder to search for clones associated with specific genomic regions. With this tool, you define a genomic region or feature (gene, STS, transcript, etc) and specify libraries of interest. Clones associated with the specified region are then displayed in assembly context. The complete list of organisms for which Clone Finder is available can be found on the Clone Finder home page.

5. What's the difference between "Total End Sequences", "Total Insert Sequences", and "Total Clones"?

-   "Total End Sequences" indicates the number of clone end sequence reads from this library that Clone DB recognizes in the NCBI Trace Archive and dbGSS. An individual clone may be associated with 0, 1, or >1 end sequence reads.
-   "Total Insert Sequences" indicates the number of clone insert sequences from this library that Clone DB recognizes in GenBank. An individual clone may be associated with 0, 1, or >1 insert sequences.
-   "Total Clones" indicates the number of clones from this library that have a record in Clone DB.

6. Where can I find information for cDNA libraries?

Clone DB is currently only storing information for genomic and cell-based libraries. Library information for cDNA libraries can still be found in the NCBI UniGene browser. cDNA library information will be migrated to Clone DB in the future.

7. Where can I find information for cell-based libraries (e.g. gene trap or gene target)?

Clone DB maintains a separate browser for cell-based libraries.

8. Where can I find information for specific clones belonging to libraries listed in the Clone DB genomic library browser?

Records for individual clones, which contain mapping, sequence and other associated information, can be accessed via Entrez searches of Clone DB. Clone DB can be searched by library/clone name, abbreviation or alias, as well as by many other terms. For a complete list of terms by which Clone DB can be searched, please see the Help page. Please note that searches for libraries will also return the records for all clones associated with that library. In addition, users can find organism-specific files listing the insert sequences for all genomic clones with records in Clone DB at the Clone DB FTP site.

9. How can I obtain a copy of a library or a clone from a library listed in the Clone DB genomic library browser?

NCBI lists known library distributors in the library browser. Users should contact these distributors directly to obtain resources. Distributor contact information is available on the Clone Registry distributor browser page. Please note: NCBI endeavors to keep distributor information up-to-date. Please contact Clone DB if you find any incorrect information.

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Last updated: 2017-12-05T21:41:45Z