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

Moriarty, John, Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239 and Metcalfe, Anthony 2007. 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. BMC Bioinformatics 8 , 70. 10.1186/1471-2105-8-70

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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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences Systems Immunity Research Institute (SIURI)
Subjects:	Q Science > Q Science (General)
Publisher:	BioMed Central
ISSN:	1471-2105
Date of First Compliant Deposit:	21 August 2018
Date of Acceptance:	2 March 2007
Last Modified:	16 May 2023 00:01
URI:	https://orca.cardiff.ac.uk/id/eprint/62733

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