Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Methodology article

Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects

John Moriarty1*, Julian R Marchesi23 and Anthony Metcalfe1

Author Affiliations

1 Department of Mathematics/Boole Centre for Research in Informatics, University College Cork, Cork, Ireland

2 Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland

3 Department of Microbiology, University College Cork, Cork, Ireland

For all author emails, please log on.

BMC Bioinformatics 2007, 8:70  doi:10.1186/1471-2105-8-70

Published: 2 March 2007

Abstract

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.