Type

Journal Article

Authors

Anthony Metcalfe
Julian R. Marchesi
John Moriarty

Subjects

Biochemistry

Topics
genetics computational biology genomic library poisson distribution chromosome mapping metabolic networks and pathways sequence alignment genomics research design

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. (2006)

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 10x 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.
Collections Ireland -> University College Cork -> PubMed

Full list of authors on original publication

Anthony Metcalfe, Julian R. Marchesi, John Moriarty

Experts in our system

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Julian R Marchesi
University College Cork
Total Publications: 45