Due to their large insert size and stability, Bacterial Artificial Chromosome (BAC) clones have emerged as an essential component in genome mapping, DNA sequencing, as well as comparative and functional genomics projects to answer evolutionary, agricultural and biomedical questions. As such, the National Science Foundation (NSF) has initiated a program that funds the construction of 31 animal BAC libraries and 32 plant BAC libraries from species spanning the phylogenetic tree of life. Clearly, these libraries should be of high quality to be most useful. Quality control therefore becomes an essential requirement. BAC end sequencing provides several pieces of critical information about a BAC library regarding contaminations, randomness and insert size. Here we propose to end sequence approximately 100 random clones from each library and conduct sequence analyses to assess the quality of the 63 BAC libraries that are being constructed under the NSF program.
