BAC End Sequencing

Large-insert genomic DNA libraries are based on the Escherichia coli F factor, a low-copy plasmid that exits in a supercoiled circular form in the host cells. These libraries are used to provide a way to divide complex genomes into DNA segments, thereby reducing the complexity (). The libraries are arrayed in microtiter dishes, providing the opportunity for many researchers to accumulate and use information regarding particular clones. The information about the end sequence of the bacterial artificial chromosome (BAC) clones is currently used in a wide array of applications from genome sequencing to gene discovery. The BAC end sequences of individual clones with insert DNA are collected in the large databases that can be accessed by the researcher. The information regarding the BAC end sequence stored in these databases makes it easier to identify the minimally overlapping clones that can be used as a source for shotgun-sequencing projects (), to find clones for restriction fingerprints for building overlapping clone sets (), to find appropriate clones for fluorescence in situ hybridization mapping (), or to select a BAC clone that contains genes of interest (). Some important BAC end sequence databases are as follows: 1. Human: http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_search.html, 470,000 clones. 2. Rice: http://www.genome.clemson.edu/projects/rice/rice_bac_end/index.html, 92,000 clones. 3. Mouse: http://www.tigr.org/tdb/bac_ends/mouse/bac_end_intro.html, 300,000 clones. 4. Rat: http://www.tigr.org/tdb/bac_ends/rat/bac_end_intro.html, 200,000 clones. 5. Sea urchin: http://sugp.caltech.edu:7000, 25,000 clones. 6. Arabidopsis thaliana: http://ftp.tigr.org/tdb/at/abe/bac_end_search.html, >40,000 clones. 7. Trypanosoma brucei: http://ftp.tigr.org/tdb/mdb/tbdb/bac_end_search.html, 10,000 clones.