Theories and applications for sequencing randomly selected clones

Theory is developed for the process of sequencing randomly selected large-i nsert clones. Genome size, library depth, clone size, and clone distributio n are considered relevant properties and perfect overlap detection For cont ig assembly is assumed. Genome-specific and nonrandom effects are neglected . Order of magnitude analysis indicates library depth is of secondary impor tance compared to the other variables, especially as clone size diminishes. In such cases, the well-known Poisson coverage law is a good approximation . Parameters derived from these models ale used to examine performance For the specific case of sequencing random human BAC clones. We compare coverag e and redundancy rates for libraries possessing uniform and nonuniform clon e distributions. Results are measured against data from map-based human-chr omosome-2 sequencing. We conclude that the map-based approach outperforms r andom clone sequencing, except early in a project. However, simultaneous us e of both strategies can be beneficial if a performance-based estimate for halting random clone sequencing is made. Results Further show that the rand om approach yields maximum effectiveness using nonbiased rather than biased libraries.