Human BAC ends quality assessment and sequence analyses

End sequences from bacterial artificial chromosomes (BACs) provide highly s pecific sequence markers in large-scale sequencing projects, To date, we ha ve generated >300,000 end sequences from >186,000 human BAC clones with an average read length of >460 bp for a total of 141 Mb covering similar to 4. 7% of the genome. Over 60% of the clones have BAC end sequences (BESs) from both ends representing more than fivefold coverage of the human genome by the paired-end clones. Our quality assessments and sequence analyses indica te that BESs from human BAC libraries developed at The California Institute of Technology (CalTech) and Roswell Park Cancer Institute have similar pro perties. The analyses have highlighted differences in insert size for diffe rent segments of the CalTech library. Problems with the fidelity of trackin g of sequence data back to physical clones have been observed in some subse ts of the overall BES dataset. The annotation results of BESs for the conte nts of available genomic sequences, sequence tagged sites, expressed sequen ce tags, protein encoding regions, and repeats indicate that this resource will be valuable in many areas of genome research. (C) 2000 Academic Press.