Abstract:
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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Stark M,Berger SA,Stamatakis A,von Mering Cdoi
10.1186/1471-2164-11-461subject
Has Abstractpub_date
2010-08-05 00:00:00pages
461issn
1471-2164pii
1471-2164-11-461journal_volume
11pub_type
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