Extension of Lander-Waterman theory for sequencing filtered DNA libraries

Background: The degree to which conventional DNA sequencing techniques will be successful for highly repetitive genomes is unclear. Investigators are therefore considering various filtering methods to select against high-copy sequence in DNA clone libraries. The standard model for random sequencing, Lander-Waterman theory, does not account for two important issues in such libraries, discontinuities and position-based sampling biases (the so-called "edge effect"). We report an extension of the theory for analyzing such configurations. Results: The edge effect cannot be neglected in most cases. Specifically, rates of coverage and gap reduction are appreciably lower than those for conventional libraries, as predicted by standard theory. Performance decreases as read length increases relative to island size. Although opposite of what happens in a conventional library, this apparent paradox is readily explained in terms of the edge effect. The model agrees well with prototype gen...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Michael C. Wendl, W. Bradley Barbazuk
• Keywords: BMCBI 2005, Edge Effect, Sequencing, Standard Theory