Clone DB FAQs

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


What is 'Clone DB'?

Clone DB is a database that integrates information about clones and libraries, including sequence data, map positions and distributor information. Clone DB has replaced the former NCBI Clone Registry, expanding the number of organisms and clone types represented. While the former Clone Registry only contained information about genomic clones and libraries, Clone DB provides integrated clone-centric information for genomic, cDNA and cell-based (gene trap/gene target) libraries and clones for a wide variety of eukaryotic organisms. New Clone DB pages will appear with the addition of data to the database. For explanations of the various Clone DB pages, please see the Help page.

What kinds of clones are found in Clone DB?

Currently, genomic and cell-based clones are represented in Clone DB. To review the complete list of available libraries, please visit the Genomic Clone Library Browser and Cell-Based Clone Library Browser. Clicking on any library name will take you to a library-specific page that will give you details about the library. Records for individual clones, which contain mapping, sequence and other associated information, can be accessed via Entrez searches of Clone DB. cDNA libraries and clones will be added to Clone DB in the future.

Clone Nomenclature: How does Clone DB manage genomic library and clone names?

Each genomic library in Clone DB is assigned a standard name and abbreviation that is unique for a given organism. Wherever possible, Clone DB adopts library names and abbreviations that have been provided to us by library creators or distributors as the standard names. In cases where a library is commonly known to a research community by more than 1 name, Clone DB assigns one of these names as the standard and stores all other known names and abbreviations as alternates. Alternate library names and abbreviations for a given library can be viewed on the corresponding library-specific record page. Clone DB can be searched using either standard clone/library names or aliases. For detailed searching information, please see the Clone DB Help page.

A genomic clone's standardized name in Clone DB is comprised of its microtiter plate address (plate number, row and column), prefixed by the standard library abbreviation, to provide a unique clone name (see below). If a non-standardized name has been provided in a clone's insert or end sequence record in an INSDC database, the non-standardized name is stored in Clone DB as an alias of the standardized name. To facilitate integration of clone-based information from various databases, Clone DB strongly recommends that insert and end sequence submissions for genomic clones to INSDC databases utilize the Clone DB standard naming scheme.

clone-naming-scheme

How can I identify a specific genomic or cell-based 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, or cell-based gene-trap and gene-targeting clones affiliated with 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.

The NCBI Clone Finder can also be used to search for genomic clones associated with specific genomic regions. With this tool, you define a genomic region or feature (gene, STS, transcript, etc) on a given assembly 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, as well as a link to the tool, can be found on the Clone Finder home page.

How can I find the insert or end sequences for a particular clone?

All clone-associated sequences are provided as part of individual clone records. Searching Clone DB by clone name will return these records. For detailed searching instructions, please see the Clone DB Help page. In addition, insert sequences for all genomic clones are provided in organism-specific reports available at the Clone DB FTP site.

How can I find all of the clones in a specific library?

Clone DB can be searched by library name, abbreviation or alias. Searches for libraries will also return the records for all clones associated with that library. For more detailed information on searching Clone DB, please see the Help page.

How does NCBI create clone placements for genomic clones?

For information on NCBI clone placements, please see the placements FAQ page.

How do I use the genomic and cell-based library browsers?

For instructions on browser usage, please see the genomic and cell-based browser FAQ pages.

How can I obtain a clone or library listed in Clone DB?

Clone DB is not a library or clone distributor. Distributor information for specific genomic libraries is provided in the library record and library browser pages, while distributor information for cell-based clones is provided only in the individual clone records. Contact information for the complete list of suppliers of genomic libraries and clones in Clone DB is available on our distributors page, as well as in individual clone records. Please note: NCBI endeavors to keep distributor information up-to-date. Please contact Clone DB if you find any incorrect information.

Where can I find information for human FISH-mapped BAC clones?

The Human BAC Resource provides data for a genome-wide collection of clones that were used as fluorescent in situ hybridization (FISH) probes to assist with integration of cytogenetic, radiation-hybrid, linkage and sequence maps of the human genome. Additional data for BAC clones that were mapped at very high resolution to the human genome is available as part of the NIH Cancer Chromosome Aberrations Project (CCAP).

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Last updated: 2017-12-05T21:48:42Z