Paper abstract


deFUME: Dynamic Exploration of Functional Metagenomic Sequencing Data
Eric van der Helm1,*, Henrik Marcus Geertz-Hansen1,2,3, Hans Jasper Genee1, Sailesh Malla1, and Morten O. A. Sommer1,4
*to whom correspondence should be addressed, e-mail:

1 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2870 Hørsholm, Denmakr
2 Center for Biological Sequence Analysis, Department of Systems Biology, , Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
3 Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denrk
4 Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark

van der Helm E, Geertz-Hansen HM, Genee HJ, Malla S, Sommer MOA: deFUME: Dynamic exploration of functional metagenomic sequencing data. BMC Res Notes 2015, 8:328


Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field.

Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface.

The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at and the source code is distributed at

Keywords: Functional metagenomics; Web services; Visualization; Sequence analysis; Gene ontology
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