dc.contributor.author |
Moriarty, John |
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dc.contributor.author |
Marchesi, Julian R. |
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dc.contributor.author |
Metcalfe, Anthony |
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dc.date.accessioned |
2012-11-29T12:27:28Z |
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dc.date.available |
2012-11-29T12:27:28Z |
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dc.date.copyright |
2007-03 |
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dc.date.issued |
2007-03-02 |
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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 |
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dc.identifier.volume |
8 |
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dc.identifier.startpage |
70 |
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dc.identifier.issn |
1471-2105 |
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dc.identifier.uri |
http://hdl.handle.net/10468/826 |
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dc.identifier.doi |
10.1186/1471-2105-8-70 |
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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. |
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dc.description.sponsorship |
Science Foundation Ireland (04/RP1/I512); Science Foundation Ireland (SFI-CSET); Irish Government (National Development Plan (2000 - 2006)) |
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dc.format.mimetype |
application/pdf |
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dc.language.iso |
en |
en |
dc.publisher |
BioMed Central |
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dc.relation.uri |
http://www.biomedcentral.com/1471-2105/8/70 |
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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), |
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dc.rights.uri |
http://creativecommons.org/licenses/by/2.0 |
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dc.subject |
Gaps |
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dc.subject |
Circles |
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dc.subject |
Lines |
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dc.subject |
Fragments |
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dc.subject |
Genomic |
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dc.subject |
Metagenomic |
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dc.subject |
Bioinformatics |
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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 |
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dc.type |
Article (peer-reviewed) |
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dc.internal.authorurl |
http://www.proba.ucc.ie/~jm20/ |
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dc.internal.authorcontactother |
Department of Mathematics/Boole Centre for Research in Informatics, University College Cork, Cork, Ireland. Email: jm20@proba.ucc.ie |
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dc.internal.availability |
Full text available |
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dc.description.version |
Published Version |
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dc.contributor.funder |
Science Foundation Ireland |
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dc.contributor.funder |
Irish Government |
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dc.description.status |
Peer reviewed |
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dc.identifier.journaltitle |
BMC Bioinformatics |
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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 |
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dc.internal.IRISemailaddress |
jm20@proba.ucc.ie |
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