Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical applicati

Background: The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distributions for the number of gaps have been given in the literature, one motivation being ease of computation. Error bounds for these approximate distributions have not been given. Results: We give bounds on the probability distribution of the number of gaps when a circle is covered by fragments of fixed size. The absolute error in the approximation is typically on the order of 0.1% at 10× coverage depth. The method can be applied to coverage problems on the interval, including edge effects, and applications are given to metagenomic libraries and shotgun sequencing. Background The question of how a circle becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. As an example, a prokaryotic chromosome is typically circular and the clones ex...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: John Moriarty, Julian R. Marchesi, Anthony Metcalfe
• Keywords: Approximate Distributions, BMCBI 2007, Shotgun Sequencing, Uncovered Gaps