The NCBI Clone Database is a replacement and expansion upon a former database entitled the NCBI Clone Registry, representing a broader range of both eukaryotic organisms and clone types. It first came to be during the era of the human and mouse genome projects (1), taking place in the 90’s and early 2000’s. This database is useful because it combines information regarding genomic clones and libraries such as genomic positions (assigning DNA fragments to chromosomes), sequence data, and distributor information (1). It contains records for genomic and cell-based libaries and clones that represent over 100 different eukaryotic species (3).
A clone is often defined as a “self-replicating system containing a DNA fragment of interest” (1). A genomic library is a collection of all the genomic DNA from one organism. Once DNA is extracted from the cells of an organism, it is digested with an enzyme that cuts it into fragments, each inserted into a vector using DNA ligase. Then, each vector molecule is taken up by a host of either bacteria or yeast. By using these hosts to carry these vectors, it is much easier to amplify and retrieve certain clones from the library for analysis (2). A cell-based library is a collection of cells or tissues, or their original organisms, that carry genetic modifications. Most commonly, these represent collections of gene trapped or gene targeting clones. In order to obtain this information, foreign DNA fragments are attached to a purified replicon. The resulting hybrid molecules are then transferred into host cells, where they replicate independently of the host cell chromosomes. Because the foreign DNA fragments can be viewed as passengers of the replicon, replicons used for cloning are typically deemed as vector molecules (1).
How to UseEdit
In the "Getting Started" column (A), you will find a few basic, helpful links. In the "Tools" column (B), you will find links specific to NCBI Clone Database, and in the "Related Resources" column (C), you will find other resources that represent Clone Database (3 ).
Under "Tools", both the "Genomic clone library browser" and the "Cell-based clone library browser" allow you to browse libraries available within the database. A list of libraries is displayed in table D under the Genomic Clone Library Browser. The letter E indicates the way in which the library is sorted, in this case being "Total clones". Clicking any header will sort the library accordingly. Additional search filters for the library are available under letter F. The Cell-Based Library Browser (G) works in a similar manner and is also filterable (H) (3 ).Searching for Clones
Specific clones can be found by simpy using the search bar (A) on top of the Clone Database homepage. The "Help" link (B) provides more details on how to use the database. Clicking "Advanced" (C) opens the "Clone Advanced Search Builder", allowing you to browse specific index fields (D) and the corresponding terms under them by clicking "Show index list" (E). Any selected query terms are entered in the query box (F), while clicking "Add to history" (G) displays the result under "History" section. "Edit" (H) unlocks the query box so that custom terms may be added (3 ).
Displaying Your Search ResultsEditAll results are located under "Tabular View". Clones and their corresponding libraries are separated into two tabs, "Clones" (I) and "Libraries" (J), both of which contain further information. Clicking "Display settings" launches a pop-up (K) which allows you to sort the information by certain means. Filters (L) are provided in the left-hand column (3 ).
Detailed Library Record ViewEdit
By searching with the term "mouse[orgn]" (A), you are able to retrieve a long list of clones. These results can be further filtered under letter B. You can click on a library name to open a detailed display (C) that provides a summary and other further details regarding the library, for example, DNA source (D). "Library Construction" (E) describes technical features of the library while "Library Statistics" (F) provides summary statistics (3 ).
Detailed Genomic Clone Record View Edit
Clones are often importantly characterized and filed by their genomic location. Clone Database maps genomic clones for easy retrieval. With the use of the search bar (A), you can find a list of clones, each with a different clone name (B), that when clicked draws up a clone summary (C) which includes genomic location. The "Genome View" tab (D) provides a genomic map of the clone by other means. If you hover the mouse over the clone placement (E), you will see a popup containing additional details. The "Clone Placements" tab (F) displays mapping data in tabular format. The "Associated Sequences" tab (G) provides records for insert and end sequences while "Distributors" (H) provides a list of vendors for the clone and their corresponding information (3 ).