Clone-based sequencing is an early methodology for genome assembly. To prepare for clone-based sequencing, researchers first generate a genomic clone library. To that end, they perform an experiment in which an enzyme digests genomic DNA (isolated from to-be-sequenced organism) into pieces. They adjust the experimental conditions so that the fragments are of desired sizes and all genomic regions are evenly represented. Subsequently, individual DNA fragments are inserted (cloned) into a cloning vector, thus creating a library of genomic DNA.

Cloning vectors used for genomic libraries support the insertion of large pieces (10’s-100’s kbps) of a foreign DNA. Researchers then propagate the resulting clones in bacterial cells to obtain sufficient amounts of DNA to conduct sequencing, either of the full insert or a short sequence from either end. Ultimately, scientists can assemble an entire (eukaryotic) genome from insert sequences of overlapping genomic clones.

The two types of cloning vectors most commonly used for generating genomic libraries are bacterial artificial chromosomes (BACs) and fosmids. Scientists maintain the physical clone library on a series of microtiter plates in which each well contains the DNA of a single clone. Clone names are typically based on their location (plate/row/column) in the library. Please refer to the Clone FAQs document where you will find details on clone nomenclature used at NCBI. Throughout the years, researchers registered many clone libraries with NCBI and deposited the associated sequences to the NCBI nucleotide sequence database.