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

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dc.contributor.author Moriarty, John
dc.contributor.author Marchesi, Julian R.
dc.contributor.author Metcalfe, Anthony
dc.date.accessioned 2012-11-29T12:27:28Z
dc.date.available 2012-11-29T12:27:28Z
dc.date.copyright 2007-03
dc.date.issued 2007-03-02
dc.identifier.citation John Moriarty, Julian R Marchesi and Anthony Metcalf. (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 doi:10.1186/1471-2105-8-70 en
dc.identifier.volume 8 en
dc.identifier.startpage 70 en
dc.identifier.issn 1471-2105
dc.identifier.uri http://hdl.handle.net/10468/826
dc.identifier.doi 10.1186/1471-2105-8-70
dc.description.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. en
dc.description.sponsorship Science Foundation Ireland (04/RP1/I512); Science Foundation Ireland (SFI-CSET); Irish Government (National Development Plan (2000 - 2006)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BioMed Central en
dc.relation.uri http://www.biomedcentral.com/1471-2105/8/70
dc.rights © 2007 Moriarty et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), en
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en
dc.subject Gaps en
dc.subject Circles en
dc.subject Lines en
dc.subject Fragments en
dc.subject Genomic en
dc.subject Metagenomic en
dc.subject Bioinformatics en
dc.title 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 en
dc.type Article (peer-reviewed) en
dc.internal.authorurl http://www.proba.ucc.ie/~jm20/ en
dc.internal.authorcontactother Department of Mathematics/Boole Centre for Research in Informatics, University College Cork, Cork, Ireland. Email: jm20@proba.ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder Irish Government en
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Bioinformatics en
dc.internal.copyrightchecked You are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work to make commercial use of the work Under the following conditions: Attribution — You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). http://creativecommons.org/licenses/by/2.0 en
dc.internal.IRISemailaddress jm20@proba.ucc.ie en


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© 2007 Moriarty et al; licensee BioMed Central Ltd.  This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), Except where otherwise noted, this item's license is described as © 2007 Moriarty et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
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