Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-1017
Raes, J; Korbel, J O; Lercher, M J; von Mering, C; Bork, P (2007). Prediction of effective genome size in metagenomic samples. Genome Biology, 8(1):R10.
View at publisher
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.
98 downloads since deposited on 11 Feb 2008
26 downloads since 12 months
|Item Type:||Journal Article, refereed, original work|
|Communities & Collections:||07 Faculty of Science > Institute of Molecular Life Sciences
08 University Research Priority Programs > Systems Biology / Functional Genomics
|Dewey Decimal Classification:||570 Life sciences; biology|
|Deposited On:||11 Feb 2008 12:20|
|Last Modified:||05 Apr 2016 12:16|
|Additional Information:||Free full text article|
Users (please log in): suggest update or correction for this item
Repository Staff Only: item control page