Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-35720
Stark, M; Berger, S A; Stamatakis, A; von Mering, C (2010). MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics, 11:461.
BACKGROUND: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS: Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. CONCLUSIONS: We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
|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
|DDC:||570 Life sciences; biology|
|Date:||5 August 2010|
|Deposited On:||04 Nov 2010 14:30|
|Last Modified:||28 Nov 2013 00:31|
|Citations:||Web of Science®. Times Cited: 36|
Scopus®. Citation Count: 38
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