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

Simple item page
dc.contributor.authorMoriarty, John
dc.contributor.authorMarchesi, Julian R.
dc.contributor.authorMetcalfe, Anthony
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderIrish Governmenten
dc.date.accessioned2012-11-29T12:27:28Z
dc.date.available2012-11-29T12:27:28Z
dc.date.copyright2007-03
dc.date.issued2007-03-02
dc.description.abstractBackground: 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.sponsorshipScience Foundation Ireland (04/RP1/I512); Science Foundation Ireland (SFI-CSET); Irish Government (National Development Plan (2000 - 2006))en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationJohn 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:10.1186/1471-2105-8-70en
dc.identifier.doi10.1186/1471-2105-8-70
dc.identifier.issn1471-2105
dc.identifier.journaltitleBMC Bioinformaticsen
dc.identifier.startpage70en
dc.identifier.urihttps://hdl.handle.net/10468/826
dc.identifier.volume8en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urihttp://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.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectGapsen
dc.subjectCirclesen
dc.subjectLinesen
dc.subjectFragmentsen
dc.subjectGenomicen
dc.subjectMetagenomicen
dc.subjectBioinformaticsen
dc.titleBounds on the distribution of the number of gaps when circles and lines are covered by fragments: theory and practical application to genomic and metagenomic projectsen
dc.typeArticle (peer-reviewed)en
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
JM_BoundsPV2007.pdf
Size:
197.14 KB
Format:
Adobe Portable Document Format
Description:
Published Version
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
2.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
APC Microbiome Ireland - Journal Articles
Mathematical Sciences- Journal Articles
Microbiology - Journal Articles